subject:( CycloMolder inclusion Complex cyclodextrin molecular modeling Molecular docking )

1. RABELLO, Marcelo Montenegro. Desenvolvimento e automação de metolodogias in silico para o estudo de complexos de inclusão utilizados na inova o terapêutica .

Degree: 2016, Universidade Federal de Pernambuco

URL: https://repositorio.ufpe.br/handle/123456789/17588

► Este trabalho apresenta uma metodologia in silico para o estudo de complexos de inclus o utilizados na inova o terap utica. Um complexo de inclus… (more)

Subjects/Keywords: Bioinform tica.Terap utica.Ciclodextrinas. CycloMolder, complexos de inclus o, ciclodextrina, modelagem molecular, docking molecular; CycloMolder, inclusion Complex, cyclodextrin, molecular modeling, Molecular docking.

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

RABELLO, M. M. (2016). Desenvolvimento e automação de metolodogias in silico para o estudo de complexos de inclusão utilizados na inova o terapêutica . (Doctoral Dissertation). Universidade Federal de Pernambuco. Retrieved from https://repositorio.ufpe.br/handle/123456789/17588

Chicago Manual of Style (16^th Edition):

RABELLO, Marcelo Montenegro. “Desenvolvimento e automação de metolodogias in silico para o estudo de complexos de inclusão utilizados na inova o terapêutica .” 2016. Doctoral Dissertation, Universidade Federal de Pernambuco. Accessed March 05, 2021. https://repositorio.ufpe.br/handle/123456789/17588.

MLA Handbook (7^th Edition):

RABELLO, Marcelo Montenegro. “Desenvolvimento e automação de metolodogias in silico para o estudo de complexos de inclusão utilizados na inova o terapêutica .” 2016. Web. 05 Mar 2021.

Vancouver:

RABELLO MM. Desenvolvimento e automação de metolodogias in silico para o estudo de complexos de inclusão utilizados na inova o terapêutica . [Internet] [Doctoral dissertation]. Universidade Federal de Pernambuco; 2016. [cited 2021 Mar 05]. Available from: https://repositorio.ufpe.br/handle/123456789/17588.

Council of Science Editors:

RABELLO MM. Desenvolvimento e automação de metolodogias in silico para o estudo de complexos de inclusão utilizados na inova o terapêutica . [Doctoral Dissertation]. Universidade Federal de Pernambuco; 2016. Available from: https://repositorio.ufpe.br/handle/123456789/17588

2. Kellici, Tahsin. Δυναμικές ιδιότητες της ολμεσαρτάνης στο διάλυμα και στο ενεργό κέντρο του υποδοχέα τύπου 1 της αγγειοτασίνης ΙΙ: βελτιστοποίηση φαρμακευτικού προφίλ βιοδραστικών ενώσεων μέσω συμπλόκων εγκλεισμού.

Degree: 2017, University of Ioannina; Πανεπιστήμιο Ιωαννίνων

URL: http://hdl.handle.net/10442/hedi/40945

► In this thesis, we utilized an array of biophysical techniques to characterize in atomic level the interactions formed in small molecules and their receptors along… (more)

▼ In this thesis, we utilized an array of biophysical techniques to characterize in atomic level the interactions formed in small molecules and their receptors along with inclusion complexes. A special emphasis was given to complement the specific studies with in silico studies. The conformational properties of olmesartan and its methylated analogue were charted using a combination of NMR spectroscopy and molecular modeling. For the molecular docking calculations three different types of angiotensin II type 1 receptor (AT1R) have been used: (a) the crystal structure; (b) a homology model based on the structure of CXCR4 and (c) a homology model based on the structure of rhodopsin. The aim of this study was to possibly explain the differences between the experimental findings derived from mutagenesis studies on this receptor and the crystal structure of the AT1R-olmesartan complex. Molecular Dynamics (MD) experiments were performed to show the stability of the AT1R-inverse agonist complex and the most prominent interactions during the simulated trajectory. The obtained results showed that olmesartan and its methyl ether exert similar interactions with critical residues justifying their almost identical in vitro activity. However, the docking and MD experiments failed to justify the mutation findings in a satisfactory matter, indicating that the real system is more complex and crystal structure or homology models of AT1R receptors cannot simulate it sufficiently. Various conformations of olmesartan and olmesartan methyl ether were simulated to provide chemical shifts. These were compared with the experimental NMR results. Useful information regarding the putative bioactive conformations of olmesartan and its methylated analogue has been obtained. Finally, comparative data regarding the binding poses and energies of olmesartan, olmesartan methyl ether and three derivative compounds of olmesartan (R239470, R781253, R794847) were acquired using Prime/MM-GBSA calculations.In silico studies, have been also utilized in an effort to determine the architecture of inclusion complexes of natural products and hosts. As host we used both different cyclodextrin derivatives as also calixarens. Specifically, the interaction between the hepatoprotectant drug silibinin and the host 2-hydroxypropyl-β-cyclodextrin (HP-β-CD) has been elucidated at the molecular level. The complexation product of silibinin with HP-β-CD has been characterized by Differential Scanning Calorimetry, solid and liquid high resolution NMR spectroscopy. The chemical shift changes using 13C CP/MAS on the complexation of the guest with the host provided significant information on the molecular interactions and they were in agreement with the 2D NOESY results. These results point out that both in solid and liquid forms, the drug is engulfed and interacts with HP-β-CD in identical manner. Molecular dynamics calculations have been conducted to explore the thermodynamic characteristics associated with the silibinin–HP-β-CD interactions and to study the stability of the…

Subjects/Keywords: Μοριακή πρόσδεση; Μοριακή δυναμική; Υποδοχέας της αγγειοτασίνης; Ενώσεις εγκλεισμού; Καλιξαρένια; Σύμπλοκα εγκλεισμού κυκλοδεξτρινών; Molecular docking; Molecular dynamics; Angiotensin II type 1 receptor; Inclusion complexes; Calixarenes; Cyclodextrin inclusion complexes

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APA (6^th Edition):

Kellici, T. (2017). Δυναμικές ιδιότητες της ολμεσαρτάνης στο διάλυμα και στο ενεργό κέντρο του υποδοχέα τύπου 1 της αγγειοτασίνης ΙΙ: βελτιστοποίηση φαρμακευτικού προφίλ βιοδραστικών ενώσεων μέσω συμπλόκων εγκλεισμού. (Thesis). University of Ioannina; Πανεπιστήμιο Ιωαννίνων. Retrieved from http://hdl.handle.net/10442/hedi/40945

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Kellici, Tahsin. “Δυναμικές ιδιότητες της ολμεσαρτάνης στο διάλυμα και στο ενεργό κέντρο του υποδοχέα τύπου 1 της αγγειοτασίνης ΙΙ: βελτιστοποίηση φαρμακευτικού προφίλ βιοδραστικών ενώσεων μέσω συμπλόκων εγκλεισμού.” 2017. Thesis, University of Ioannina; Πανεπιστήμιο Ιωαννίνων. Accessed March 05, 2021. http://hdl.handle.net/10442/hedi/40945.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Kellici, Tahsin. “Δυναμικές ιδιότητες της ολμεσαρτάνης στο διάλυμα και στο ενεργό κέντρο του υποδοχέα τύπου 1 της αγγειοτασίνης ΙΙ: βελτιστοποίηση φαρμακευτικού προφίλ βιοδραστικών ενώσεων μέσω συμπλόκων εγκλεισμού.” 2017. Web. 05 Mar 2021.

Vancouver:

Kellici T. Δυναμικές ιδιότητες της ολμεσαρτάνης στο διάλυμα και στο ενεργό κέντρο του υποδοχέα τύπου 1 της αγγειοτασίνης ΙΙ: βελτιστοποίηση φαρμακευτικού προφίλ βιοδραστικών ενώσεων μέσω συμπλόκων εγκλεισμού. [Internet] [Thesis]. University of Ioannina; Πανεπιστήμιο Ιωαννίνων; 2017. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/10442/hedi/40945.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Kellici T. Δυναμικές ιδιότητες της ολμεσαρτάνης στο διάλυμα και στο ενεργό κέντρο του υποδοχέα τύπου 1 της αγγειοτασίνης ΙΙ: βελτιστοποίηση φαρμακευτικού προφίλ βιοδραστικών ενώσεων μέσω συμπλόκων εγκλεισμού. [Thesis]. University of Ioannina; Πανεπιστήμιο Ιωαννίνων; 2017. Available from: http://hdl.handle.net/10442/hedi/40945

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

3. Dambrauskaitė, Justė. Α-galaktozilkeramido analogų paieška ir molekulinis modeliavimas.

Degree: Master, Pharmacy, 2011, Lithuanian Academic Libraries Network (LABT)

URL: http://vddb.laba.lt/obj/LT-eLABa-0001:E.02~2011~D_20110628_151249-79556 ;

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Vykdytas tyrimas, kurio tikslas - atlikti junginių - α-GalCer analogų – paiešką. Analogai turėtų pasižymėti α-GalCer agonistiniu poveikiu NKT ląstelėms, tačiau, skirtingai nei α-GalCer, neturėtų… (more)

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Vykdytas tyrimas, kurio tikslas - atlikti junginių - α-GalCer analogų – paiešką. Analogai turėtų pasižymėti α-GalCer agonistiniu poveikiu NKT ląstelėms, tačiau, skirtingai nei α-GalCer, neturėtų būti toksiški. Ieškomi junginiai – potencialios vaistinės medžiagos, skirtos opinio kolito ir kitų uždegiminių žarnyno ligų gydymui. Atlikus atitinkamos mokslinės literatūros analizę, išnagrinėjus α-GalCer bei baltymo CD1d struktūrą, jų jungimosi ypatumus ir reikalavimus junginio, kuris galėtų pakeisti α-GalCer, struktūrai, sumodeliuoti junginiai, kurie ištirti kompleksacijos būdu. Kompleksacijos proceso metu atrinkti šeši junginiai, kurie panašiausiai į α-GalCer jungiasi su baltymu CD1d bei turėtų pasižymėti pageidaujamomis savybėmis. Šių junginių struktūros pasiūlytos sintezei.

The aim of investigation performed is to propose possible analogues of α-GalCer. The analogues must have same beneficial properties as α-GalCer except the toxicity. The compounds we are looking for is a potential therapeutic agents to treat ulcerative colitis and other inflamatory bowel diseases. After studying scietific literature, the structure of α-GalCer and protein CD1d, their binding properties, and the requirements for the structure of possible analogue of α-GalCer, we accomplished molecular modeling of several compounds and performed docking. Docking revealed six compounds that are the most believable to have same binding properties with CD1d as α-GalCer does and same therapeutic properties. The structures of those compounds were proposed for a synthesis and other examination will be performed later.

Advisors/Committee Members: Briedis, Vitalis (Master’s thesis supervisor), Petrikaitė, Vilma (Master’s thesis reviewer), Tarasevičius, Eduardas (Master’s degree committee chair), Lukošius , Audronis (Master’s degree committee member), Janulis, Valdimaras (Master’s degree committee member), Ivanauskas, Liudas (Master’s degree committee member), Savickas, Arūnas (Master’s degree committee member), Briedis , Vitalis (Master’s degree committee member), Ramanauskienė , Kristina (Master’s degree committee member), Radžiūnas , Raimondas (Master’s degree committee member), Pečiūra , Rimantas (Master’s degree committee member), Gumbrevičius, Gintautas (Master’s degree committee member), Rodovičius , Hiliaras (Master’s degree committee member).

Subjects/Keywords: Molekulinis; Modeliavimas; Kompleksacija; Molecular; Modeling; Docking

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Dambrauskaitė, Justė. (2011). Α-galaktozilkeramido analogų paieška ir molekulinis modeliavimas. (Masters Thesis). Lithuanian Academic Libraries Network (LABT). Retrieved from http://vddb.laba.lt/obj/LT-eLABa-0001:E.02~2011~D_20110628_151249-79556 ;

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Chicago Manual of Style (16^th Edition):

Dambrauskaitė, Justė. “Α-galaktozilkeramido analogų paieška ir molekulinis modeliavimas.” 2011. Masters Thesis, Lithuanian Academic Libraries Network (LABT). Accessed March 05, 2021. http://vddb.laba.lt/obj/LT-eLABa-0001:E.02~2011~D_20110628_151249-79556 ;.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

MLA Handbook (7^th Edition):

Dambrauskaitė, Justė. “Α-galaktozilkeramido analogų paieška ir molekulinis modeliavimas.” 2011. Web. 05 Mar 2021.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Vancouver:

Dambrauskaitė, Justė. Α-galaktozilkeramido analogų paieška ir molekulinis modeliavimas. [Internet] [Masters thesis]. Lithuanian Academic Libraries Network (LABT); 2011. [cited 2021 Mar 05]. Available from: http://vddb.laba.lt/obj/LT-eLABa-0001:E.02~2011~D_20110628_151249-79556 ;.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Council of Science Editors:

Dambrauskaitė, Justė. Α-galaktozilkeramido analogų paieška ir molekulinis modeliavimas. [Masters Thesis]. Lithuanian Academic Libraries Network (LABT); 2011. Available from: http://vddb.laba.lt/obj/LT-eLABa-0001:E.02~2011~D_20110628_151249-79556 ;

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Duquesne University

4. Raghavan, Sudhir. Synthesis and Molecular Modeling Studies of Bicyclic Inhibitors of Dihydrofolate Reductase, Receptor Tyrosine Kinases and Tubulin.

Degree: PhD, Medicinal Chemistry, 2013, Duquesne University

URL: https://dsc.duq.edu/etd/1080

► The results from this work are reported into two sections listed below: Synthesis: Following structural classes of compounds have been designed, synthesized and studied as… (more)

▼ The results from this work are reported into two sections listed below: Synthesis: Following structural classes of compounds have been designed, synthesized and studied as inhibitors of pjDHFR, RTKs and tubulin: 1. 2,4-Diamino-6-(substituted-arylmethyl)pyrido[2,3-d]pyrimidines 2. 4-((3-Bromophenyl)linked)-6-(substituted-benzyl)-7H-pyrrolo[2,3-d]pyrimidin-2-amines 3. 6-Methyl-5-((substitutedphenyl)thio)-7H-pyrrolo[2,3-d]pyrimidin-2-amines A total of 35 new compounds (excluding intermediates) were synthesized, characterized and submitted for biological evaluation. Results from these studies will be presented in due course. Bulk synthesis of the potent lead compound 170 was carried out to facilitate in vivo evaluation. Docking Studies Docking studies were performed using LeadIT, MOE, Sybyl or Flexx for target compounds listed above and for other compounds reported by Gangjee et al. against the following targets: 1. Dihydrofolate reductase: human, P. carinii, P. jirovecii (pjDHFR) and T. gondii (tgDHFR) 2. Thymidylate synthase: human (hTS) and T. gondii (tgTS) 3. Receptor tyrosine kinases: VEGFR2, EGFR and PDGFR-β 4. Colchicine binding site of tublulin. Novel homology models were generated and validated for pjDHFR, tgDHFR, tgTS, PDGFR-β and the F36C L65P pjDHFR double mutant. The tgTS homology model generated in this study and employed to design novel inhibitors shows remarkable similarity with the recently published X-ray crystal structures. Docking studies were performed to provide a molecular basis for the observed activity of target compounds against DHFR, RTKs or tubulin. Results from these studies support structure-based and ligand-based medicinal chemistry efforts in order to improve potency and/or selectivity of analogs of the docked compounds against these targets. Novel topomer CoMFA models were developed for tgTS and hTS using a set of 85 bicyclic inhibitors and for RTKs using a set of 60 inhibitors reported by Gangjee et al. The resultant models could be used to explain the potency and/or selectivity differences for selected molecules for tgTS over hTS. Topomer CoMFA maps show differences in steric and/or electronic requirements among the three RTKs, and could be used, in conjuction with other medicinal chemistry approaches, to modulate the selectivity and/or potency of inhibitors with multiple RTK inhibitory potential. Drug design efforts that involve virtual library screening using these topomer CoMFA models in conjunction with traditional medicinal chemistry techniques and docking are currently underway. Advisors/Committee Members: Aleem Gangjee, Marc Harrold, Patrick Flaherty, David Lapinsky, Lawrence Block, James Drennen, J. Douglas Bricker.

Subjects/Keywords: Cancer; Docking; Homology modeling; Molecular modeling; Opportunistic infections

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Raghavan, S. (2013). Synthesis and Molecular Modeling Studies of Bicyclic Inhibitors of Dihydrofolate Reductase, Receptor Tyrosine Kinases and Tubulin. (Doctoral Dissertation). Duquesne University. Retrieved from https://dsc.duq.edu/etd/1080

Chicago Manual of Style (16^th Edition):

Raghavan, Sudhir. “Synthesis and Molecular Modeling Studies of Bicyclic Inhibitors of Dihydrofolate Reductase, Receptor Tyrosine Kinases and Tubulin.” 2013. Doctoral Dissertation, Duquesne University. Accessed March 05, 2021. https://dsc.duq.edu/etd/1080.

MLA Handbook (7^th Edition):

Raghavan, Sudhir. “Synthesis and Molecular Modeling Studies of Bicyclic Inhibitors of Dihydrofolate Reductase, Receptor Tyrosine Kinases and Tubulin.” 2013. Web. 05 Mar 2021.

Vancouver:

Raghavan S. Synthesis and Molecular Modeling Studies of Bicyclic Inhibitors of Dihydrofolate Reductase, Receptor Tyrosine Kinases and Tubulin. [Internet] [Doctoral dissertation]. Duquesne University; 2013. [cited 2021 Mar 05]. Available from: https://dsc.duq.edu/etd/1080.

Council of Science Editors:

Raghavan S. Synthesis and Molecular Modeling Studies of Bicyclic Inhibitors of Dihydrofolate Reductase, Receptor Tyrosine Kinases and Tubulin. [Doctoral Dissertation]. Duquesne University; 2013. Available from: https://dsc.duq.edu/etd/1080

5. Ismail, Alexandre. Molecular modeling of Coq6, a ubiquinone biosynthesis flavin-dependent hydroxylase. Evidence of a substrate access channel : Modélisation moléculaire de Coq6, une hydroxylase flavine-dépendante de la biosynthèse de l'ubiquinone.

Degree: Docteur es, Biochimie – Modélisation moléculaire, 2016, Université Pierre et Marie Curie – Paris VI

URL: http://www.theses.fr/2016PA066044

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Coq6 est une enzyme impliquée dans la biosynthèse du coenzyme Q (aussi nommé ubiquinone, ou Q), un lipide benzoquinone polyprenylé essentiel à la fonction de… (more)

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Coq6 est une enzyme impliquée dans la biosynthèse du coenzyme Q (aussi nommé ubiquinone, ou Q), un lipide benzoquinone polyprenylé essentiel à la fonction de la chaîne respiratoire mitochondriale. Dans la levure Saccharomyces cerevisiae, cette monooxygénase flavine-dépendante putatif est proposé pour hydroxyler le noyau benzénique d' un précurseur du coenzyme Q à la position C5. Nous montrons ici à travers des études biochimiques que Coq6 est une flavoprotéine utilisant le FAD comme cofacteur. Des modèles d'homologie du complexe Coq6-FAD ont étés réalisés et étudiés par dynamique moléculaire et arrimage moléculaire du 3-hexaprenyl-4-hydroxyphényl (4-HP6), un substrat modèle hydrophobe et volumineux. Nous identifions un canal d'accès putatif pour Coq6 dans un modèle de la forme sauvage et proposons des mutations in silico positionnés à l'entrée capable de partiellement (les mutations simples G248R et L382E) ou complètement (une double-mutation G248R-L382E) bloquer l'accès du substrat au site actif via le canal d' accès. Des essais in vivo soutiennent les prédictions in silico, qui expliquent l'abrogation ou la diminution des enzymes mutées. Ce travail fournit la première information structurale détaillée d'une enzyme importante et hautement conservée de biosynthèse de l'ubiquinone.

Coq6 is an enzyme involved in the biosynthesis of coenzyme Q, a polyisoprenylated benzoquinone lipid essential to the function of the mitochondrial respiratory chain. In the yeast Saccharomyces cerevisiae, this putative flavin-dependent monooxygenase is proposed to hydroxylate the benzene ring of coenzyme Q (ubiquinone) precursor at position C5. We show here through biochemical studies that Coq6 is a flavoprotein using FAD as a cofactor. Homology models of the Coq6-FAD complex are constructed and studied through molecular dynamics and substrate docking calculations of 3-hexaprenyl-4-hydroxyphenol (4-HP6), a bulky hydrophobic model substrate. We identify a putative access channel for Coq6 in a wild type model and propose in silico mutations positioned at its entrance capable of partially (G248R and L382E single mutations) or completely (a G248R-L382E double-mutation) blocking access of the substrate to thechannel . Further in vivo assays support the computational predictions, thus explaining the decreased activities or inactivation of the mutated enzymes. This work provides the first detailed structural information of an important and highly conserved enzyme of ubiquinone biosynthesis.

Advisors/Committee Members: Mellot-Draznieks, Caroline (thesis director).

Subjects/Keywords: Enzyme; Ubiquinone; Coq6; Dynamique moléculaire; Hydroxylase; Docking; Coq6; Molecular modeling; Docking; 572.7

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ismail, A. (2016). Molecular modeling of Coq6, a ubiquinone biosynthesis flavin-dependent hydroxylase. Evidence of a substrate access channel : Modélisation moléculaire de Coq6, une hydroxylase flavine-dépendante de la biosynthèse de l'ubiquinone. (Doctoral Dissertation). Université Pierre et Marie Curie – Paris VI. Retrieved from http://www.theses.fr/2016PA066044

Chicago Manual of Style (16^th Edition):

Ismail, Alexandre. “Molecular modeling of Coq6, a ubiquinone biosynthesis flavin-dependent hydroxylase. Evidence of a substrate access channel : Modélisation moléculaire de Coq6, une hydroxylase flavine-dépendante de la biosynthèse de l'ubiquinone.” 2016. Doctoral Dissertation, Université Pierre et Marie Curie – Paris VI. Accessed March 05, 2021. http://www.theses.fr/2016PA066044.

MLA Handbook (7^th Edition):

Ismail, Alexandre. “Molecular modeling of Coq6, a ubiquinone biosynthesis flavin-dependent hydroxylase. Evidence of a substrate access channel : Modélisation moléculaire de Coq6, une hydroxylase flavine-dépendante de la biosynthèse de l'ubiquinone.” 2016. Web. 05 Mar 2021.

Vancouver:

Ismail A. Molecular modeling of Coq6, a ubiquinone biosynthesis flavin-dependent hydroxylase. Evidence of a substrate access channel : Modélisation moléculaire de Coq6, une hydroxylase flavine-dépendante de la biosynthèse de l'ubiquinone. [Internet] [Doctoral dissertation]. Université Pierre et Marie Curie – Paris VI; 2016. [cited 2021 Mar 05]. Available from: http://www.theses.fr/2016PA066044.

Council of Science Editors:

Ismail A. Molecular modeling of Coq6, a ubiquinone biosynthesis flavin-dependent hydroxylase. Evidence of a substrate access channel : Modélisation moléculaire de Coq6, une hydroxylase flavine-dépendante de la biosynthèse de l'ubiquinone. [Doctoral Dissertation]. Université Pierre et Marie Curie – Paris VI; 2016. Available from: http://www.theses.fr/2016PA066044

6. Nicolau Junior, Nilson. Diferenças Estruturais e \"Docking\" Receptor-Ligante da Proteína E7 do Vírus do Papiloma Humano (HPV) de Alto e Baixo Riscos para o Câncer Cervical.

Degree: PhD, Genética, 2013, University of São Paulo

URL: http://www.teses.usp.br/teses/disponiveis/17/17135/tde-13062013-092311/ ;

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O câncer cervical afeta milhões de mulheres em todo o mundo a cada ano. A maioria dos casos de câncer cervical é causada pelo vírus… (more)

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O câncer cervical afeta milhões de mulheres em todo o mundo a cada ano. A maioria dos casos de câncer cervical é causada pelo vírus do papiloma humano (HPV) que é sexualmente transmissível. Cerca de 40 tipos de HPV infectam o colo do útero e estes são designados como sendo de alto ou de baixo risco com base no seu potencial para provocar lesões de alto grau e câncer. A oncoproteína E7 do HPV está diretamente envolvida no aparecimento de câncer de colo do útero. Esta se associada com a proteína pRb e outros alvos celulares que promovem a imortalização celular e carcinogênese. Apesar de muito progresso nos estudos sobre os HPVs de alto risco, ainda não existe uma terapêutica adequada para o tratamento das lesões e câncer causados por este vírus. Este trabalho teve como objetivo entender as diferenças estruturais entre E7 de alto e baixo risco e sugerir, através de análises de bioinformática, possíveis sítios de ligação e inibidores para a E7. Esta é a primeira descrição da modelagem e análise de dinâmica molecular de quatro estruturas tridimensionais completas da E7 dos tipos de alto risco (HPV tipos 16 e 18), de baixo risco (HPV tipo 11) e não relacionadas ao câncer cervical (HPV tipo 1A). Os modelos foram construídos por uma abordagem híbrida usando modelagem por homologia e ab initio. Os modelos foram usados em simulações de dinâmica molecular por 50 ns, sob condições normais de temperatura e pressão. A desordem intrínseca da sequência da proteína E7 foi avaliada com o uso de ferramentas in silico. Os domínios N-terminal de todas as E7 estudadas, mesmo as de alto risco, exibiram estruturas secundárias depois da modelagem. Nas análises da trajetória da dinâmica molecular, as E7s dos HPVs dos tipos 16 e 18 apresentaram maior instabilidade nos seus domínios N-terminais em relação aos do HPV dos tipos 11 e 01. No entanto, esta variação não afetou a conformação das estruturas secundárias durante a simulação. A análise com ANCHOR indicou que as regiões CR1 e CR2 regiões dos tipos de HPV 16 e 18 contêm possíveis alvos para a descoberta da droga. Já a região CR3 do domínio C-terminal indicou estabilidade nas análises in silico e, por isso, foi usada como alvo de busca de modelos farmacofóricos e docking macromolecular. A proteína usada como modelo foi a E7 do HPV tipo 45 resultante de análises de ressonância magnética nuclear (RMN) e depositada no banco de dados de proteína (ID: 2F8B). Foram selecionados por análises sequenciais de busca farmacofórica, docking e re-docking, 19 compostos (extraídos de amplas bibliotecas de pequenos ligantes) com potencial para candidatos a inibidores da E7. Eles foram avaliados quanto a sua função de pontuação, mapas de interação receptor-ligante e toxicidade e os melhores foram indicados para estudos futuros.

Cervical cancer affects millions of women around the world each year. Most cases of cervical cancer are caused by human papilloma virus (HPV) which is sexually transmitted. About 40 types of HPV infect the cervix and these are designated as being at high or low risk based on their…

Advisors/Committee Members: Giuliatti, Silvana.

Subjects/Keywords: Desordem intrínseca; Dinâmica molecular; Docking; Docking; E7; E7; Farmacóforos; HPV; HPV; Intrinsically disorder; Macromolecular modeling; Modelagem macromolecular; Molecular dynamics; Pharmacophores

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Nicolau Junior, N. (2013). Diferenças Estruturais e \"Docking\" Receptor-Ligante da Proteína E7 do Vírus do Papiloma Humano (HPV) de Alto e Baixo Riscos para o Câncer Cervical. (Doctoral Dissertation). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/17/17135/tde-13062013-092311/ ;

Chicago Manual of Style (16^th Edition):

Nicolau Junior, Nilson. “Diferenças Estruturais e \"Docking\" Receptor-Ligante da Proteína E7 do Vírus do Papiloma Humano (HPV) de Alto e Baixo Riscos para o Câncer Cervical.” 2013. Doctoral Dissertation, University of São Paulo. Accessed March 05, 2021. http://www.teses.usp.br/teses/disponiveis/17/17135/tde-13062013-092311/ ;.

MLA Handbook (7^th Edition):

Nicolau Junior, Nilson. “Diferenças Estruturais e \"Docking\" Receptor-Ligante da Proteína E7 do Vírus do Papiloma Humano (HPV) de Alto e Baixo Riscos para o Câncer Cervical.” 2013. Web. 05 Mar 2021.

Vancouver:

Nicolau Junior N. Diferenças Estruturais e \"Docking\" Receptor-Ligante da Proteína E7 do Vírus do Papiloma Humano (HPV) de Alto e Baixo Riscos para o Câncer Cervical. [Internet] [Doctoral dissertation]. University of São Paulo; 2013. [cited 2021 Mar 05]. Available from: http://www.teses.usp.br/teses/disponiveis/17/17135/tde-13062013-092311/ ;.

Council of Science Editors:

Nicolau Junior N. Diferenças Estruturais e \"Docking\" Receptor-Ligante da Proteína E7 do Vírus do Papiloma Humano (HPV) de Alto e Baixo Riscos para o Câncer Cervical. [Doctoral Dissertation]. University of São Paulo; 2013. Available from: http://www.teses.usp.br/teses/disponiveis/17/17135/tde-13062013-092311/ ;

7. Josiane Enevina Mendes. Docking de herbicidas na glutationa transferase tau4-4 de soja (Glycine max).

Degree: 2011, Universidade Federal de São Carlos

URL: http://www.bdtd.ufscar.br/htdocs/tedeSimplificado//tde_busca/arquivo.php?codArquivo=4181

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Este estudo, baseado em docking molecular, descreve a busca das conformações mais favoráveis para a formação dos complexos alvo-ligante com herbicidas utilizados no cultivo de… (more)

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Este estudo, baseado em docking molecular, descreve a busca das conformações mais favoráveis para a formação dos complexos alvo-ligante com herbicidas utilizados no cultivo de soja e uma enzima envolvida no processo de desintoxicação, e baseado nestes resultados são propostas algumas diretrizes para o desenvolvimento de novos compostos. A proteína estudada foi a glutationa transferase Tau de soja, a GmGSTU4-4. Foram estudados 14 herbicidas: diclofope, fluazifope, cletodim, clomazona, diquate, paraquate, atrazina, diurom, bentazona, acifluorofem, fomesafem, sulfentrazona, clorimurom e glifosato. A escolha dos herbicidas se baseou na lista daqueles que são utilizados na cultura da soja e estão registrados no Ministério da Agricultura e Abastecimento do Brasil. Foram obtidos os complexos GmGSTU4-4-herbicidas. O sítio de ligação analisado por visualização molecular mostra uma forma quase cilíndrica, aberta e exposta ao solvente e composto de dois sítios G e H. No sítio G foram observadas três moléculas de água que participam de interações moleculares com vários dos herbicidas estudados o que sugere que novos compostos poderiam ser desenvolvidos observando a necessidade da presença de grupos químicos capazes de interagir com a água, tanto como doadores como aceptores de ligações de hidrogênio. Os herbicidas maiores podem ocupar os sítio G e H e parecem ser mais promissores na atividade de desintoxicação.

This study, based on molecular docking, describes the search for the most favorable conformations when complexes between herbicides, used in soybean cultivation, and an enzyme involved in the detoxification process are formed and based on these results some guidelines for the developing of new compounds are proposed. The glutathione transferase Tau, GmGSTU4-4, from soybean was the target protein, and diclofop, fluazifop, Clethodim, clomazone, diquat, paraquat, atrazine, diuron, bentazone, acifluorofem, fomesafem, sulfentrazone, glyphosate and clorimurom, the 14 herbicides studied. These last ones were chosen based on the list of those that are used in soybean crops and are registered with the Ministry of Agriculture and Supply of Brasil. For all of them the GmGSTU4-4-herbicide complexes were obtained. The protein binding site, analyzed by molecular visualization, presents an almost cylindrical shape, open and exposed to the solvent and is composed of two sites G and H. Three water molecules were observed in the G-site in that participate in molecular interactions with several of the studied herbicides, This finding suggests that new compounds that could, and should, be developed need to have in their structure chemical groups capable of interacting with the water, both as donors and acceptors of hydrogen bonds. Another interesting finding was that the largest herbicides may occupy both the G and H sites, and seem to be most promising in the activity of detoxification.

Advisors/Committee Members: Júlio Zukerman Schpector.

Subjects/Keywords: Biotecnologia; Modelagem molecular; Desintoxicação metabólica; Docking; Herbicidas; OUTROS; Docking; Molecular Modeling; Herbicides; Glutathione transferase Tau; Glutationa transferase Tau

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Mendes, J. E. (2011). Docking de herbicidas na glutationa transferase tau4-4 de soja (Glycine max). (Thesis). Universidade Federal de São Carlos. Retrieved from http://www.bdtd.ufscar.br/htdocs/tedeSimplificado//tde_busca/arquivo.php?codArquivo=4181

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Mendes, Josiane Enevina. “Docking de herbicidas na glutationa transferase tau4-4 de soja (Glycine max).” 2011. Thesis, Universidade Federal de São Carlos. Accessed March 05, 2021. http://www.bdtd.ufscar.br/htdocs/tedeSimplificado//tde_busca/arquivo.php?codArquivo=4181.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Mendes, Josiane Enevina. “Docking de herbicidas na glutationa transferase tau4-4 de soja (Glycine max).” 2011. Web. 05 Mar 2021.

Vancouver:

Mendes JE. Docking de herbicidas na glutationa transferase tau4-4 de soja (Glycine max). [Internet] [Thesis]. Universidade Federal de São Carlos; 2011. [cited 2021 Mar 05]. Available from: http://www.bdtd.ufscar.br/htdocs/tedeSimplificado//tde_busca/arquivo.php?codArquivo=4181.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Mendes JE. Docking de herbicidas na glutationa transferase tau4-4 de soja (Glycine max). [Thesis]. Universidade Federal de São Carlos; 2011. Available from: http://www.bdtd.ufscar.br/htdocs/tedeSimplificado//tde_busca/arquivo.php?codArquivo=4181

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

8. Paulo Roberto Gabbai Armelin. Modelagem molecular de derivados pirimidínicos e estudos de docking nas enzimas ciclooxigenase 1 e ciclooxigenase 2.

Degree: 2010, Universidade Federal de São Carlos

URL: http://www.bdtd.ufscar.br/htdocs/tedeSimplificado//tde_busca/arquivo.php?codArquivo=4191

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Neste trabalho, o docking molecular foi utilizado para o estudo da formação de complexos alvoligante das enzimas Ciclooxigenase 1 (COX-1) e Ciclooxigenase 2 (COX-2) com… (more)

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Neste trabalho, o docking molecular foi utilizado para o estudo da formação de complexos alvoligante das enzimas Ciclooxigenase 1 (COX-1) e Ciclooxigenase 2 (COX-2) com derivados pirimidínicos, com a finalidade de entender os possíveis mecanismos de ação e, assim, propor modificações nos compostos visando diminuir prováveis efeitos colaterais. Os ligantes escolhidos foram uma série de 25 pirimidinas substituídas com atividade conhecida. As estruturas tridimensionais destas moléculas foram obtidas por modelagem molecular e as das enzimas dos bancos de dados PDB e PDBSum sob o código 2OYE e 1CX2 para COX-1 e COX- 2 respectivamente. Os sítios de ligação escolhidos para os cálculos de docking foram de 20 Å ao redor dos ligantes cristalográficos IM8-700 (2OYE) e SC-558 (1CX2). Das pirimidinas analisadas as que formaram complexo com a COX-1 se orientaram com a porção SO2Me formando ligações de hidrogênio com a Ile517 e Phe518. Sendo o benzo[b]tiofen-2-ilmetil-2-(4- metanosulfonilfenil)-6-trifluorometilpirimidina-4-il]amina o mais favorável para a formação de complexo com a COX-1. Para a COX-2, os compostos que se ligaram mostram um padrão que inclui ligações de hidrogênio entre a porção SO2Me e a His90 e Arg513 do bolso lateral e entre a Arg120 e Tyr355 com os grupos substituintes do anel pirimidínico. A presença de um pequeno bolso lipofílico na COX-2 e os resultados de docking permitem sugerir que os ligantes 2, 15, 17, 22 e 23 poderiam mostrar melhor atividade mediante a adição de um grupo hidrofóbico no anel fenila ou tiofenila para que este grupo se posicione dentro desse bolso. Em ambos os casos o tipo de inibição provável é o competitivo. Como a busca por novos fármacos antiinflamatórios deve lidar com um equilíbrio entre a inibição de COX-2 e COX-1, os ligantes 2 e 22 que apresentaram resultados favoráveis para a COX-2 e não tanto para a COX-1 seriam os mais promissores e, portanto, aqueles que poderiam ser testados in vivo.

In this research molecular docking was used to study enzime-ligand complexes of Cyclooxygenase 1 (COX-1) and Cyclooxygenase 2 (COX-2) with pyrimidine derivatives, aiming at understanding the possible mechanisms of action of these compounds and, thus, suggest modifications that could increase their specificity. The chosen ligands were a series of 25 substituted pyrimidines with known activity. The three-dimensional structures of these compounds were obtained by molecular modeling and that of the enzymes from the PDB and PDBSum under the codes 2OYE and 1CX2 for COX-1 and COX-2 respectively. The binding sites chosen for the docking studies were 20 Å around the crystallographic ligands IM8-700 (2OYE) and SC-558 (1CX2). In the COX-1 formed complexes the SO2Me moiety is positioned in such a way as to form hydrogen bonds with Ile517 and Phe518. The benzo[b]thiophen-2-ylmethyl-[2-(4-methanesulfonylphenyl)-6-trifluoromethylpyrimidin-4- yl]amine formed the most favorable complex with COX-1. In COX-2, the enzyme-ligand interaction pattern shows the SO2Me group in the side pocket, forming hydrogen bonds…

Advisors/Committee Members: Júlio Zukerman Schpector.

Subjects/Keywords: Biotecnologia; Ciclooxigenase 1; Ciclooxigenase 2; Pirimidinas; Docking; Docking; OUTROS; Modelagem molecular; Cyclooxygenase 1; Cyclooxygenase 2; Pyrimidines; Molecular modeling

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Armelin, P. R. G. (2010). Modelagem molecular de derivados pirimidínicos e estudos de docking nas enzimas ciclooxigenase 1 e ciclooxigenase 2. (Thesis). Universidade Federal de São Carlos. Retrieved from http://www.bdtd.ufscar.br/htdocs/tedeSimplificado//tde_busca/arquivo.php?codArquivo=4191

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Armelin, Paulo Roberto Gabbai. “Modelagem molecular de derivados pirimidínicos e estudos de docking nas enzimas ciclooxigenase 1 e ciclooxigenase 2.” 2010. Thesis, Universidade Federal de São Carlos. Accessed March 05, 2021. http://www.bdtd.ufscar.br/htdocs/tedeSimplificado//tde_busca/arquivo.php?codArquivo=4191.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Armelin, Paulo Roberto Gabbai. “Modelagem molecular de derivados pirimidínicos e estudos de docking nas enzimas ciclooxigenase 1 e ciclooxigenase 2.” 2010. Web. 05 Mar 2021.

Vancouver:

Armelin PRG. Modelagem molecular de derivados pirimidínicos e estudos de docking nas enzimas ciclooxigenase 1 e ciclooxigenase 2. [Internet] [Thesis]. Universidade Federal de São Carlos; 2010. [cited 2021 Mar 05]. Available from: http://www.bdtd.ufscar.br/htdocs/tedeSimplificado//tde_busca/arquivo.php?codArquivo=4191.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Armelin PRG. Modelagem molecular de derivados pirimidínicos e estudos de docking nas enzimas ciclooxigenase 1 e ciclooxigenase 2. [Thesis]. Universidade Federal de São Carlos; 2010. Available from: http://www.bdtd.ufscar.br/htdocs/tedeSimplificado//tde_busca/arquivo.php?codArquivo=4191

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

McMaster University

9. Khadka, Bijendra. Structural and Functional Aspects of Evolutionarily Conserved Signature Indels in Protein Sequences.

Degree: PhD, 2019, McMaster University

URL: http://hdl.handle.net/11375/25115

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Analysis of genome sequences is enabling identification of numerous novel characteristics that provide valuable means for genetic and biochemical studies. Of these characteristics, Conserved Signature… (more)

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Analysis of genome sequences is enabling identification of numerous novel characteristics that provide valuable means for genetic and biochemical studies. Of these characteristics, Conserved Signature Indels (CSIs) in proteins which are specific for a given group of organisms have proven particularly useful for evolutionary and biochemical studies. My research work focused on using comparative genomics techniques to identify a large number of CSIs which are distinctive characteristics of fungi and other important groups of organisms. These CSIs were utilized to understand the evolutionary relationships among different proteins (species), and also regarding their structural features and functional significance. Based on multiple CSIs that I have identified for the PIP4K/PIP5K family of proteins, different isozymes of these proteins and also their subfamilies can now be reliably distinguished in molecular terms. Further, the species distribution of CSIs in the PIP4K/PIP5K proteins and phylogenetic analyses of these protein sequences, my work provides important insights into the evolutionary history of this protein family. The functional significance of one of the CSI in the PIP5K proteins, specific for the Saccharomycetaceae family of fungi, was also investigated. The results from structural analysis and molecular dynamics (MD) simulation studies show that this 8 aa CSI plays an important role in facilitating the binding of fungal PIP5K protein to the membrane surface. In other work, we identified multiple highly-specific CSIs in the phosphoketolase (PK) proteins, which clearly distinguish the bifunctional form of PK found in bifidobacteria from its homologs (monofunctional) found in other organisms. Structural analyses and docking studies with these proteins indicate that the CSIs in bifidobacterial PK, which are located on the subunit interface, play a role in the formation/stabilization of the protein dimer. We have also identified 2 large CSIs in SecA proteins that are uniquely found in thermophilic species from two different phyla of bacteria. Detailed bioinformatics analyses on one of these CSIs show that a number of residues from this CSI, through their interaction with a conserved network of water molecules, play a role in stabilizing the binding of ADP/ATP to the SecA protein at high temperature. My work also involved developing an integrated software pipeline for homology modeling of proteins and analyzing the location of CSIs in protein structures. Overall, my thesis work establishes the usefulness of CSIs in protein sequences as valuable means for genetic, biochemical, structural and evolutionary studies.

Dissertation

Doctor of Philosophy (PhD)

Advisors/Committee Members: Gupta, Radhey S., Biochemistry and Biomedical Sciences.

Subjects/Keywords: Genomics; Molecular Signatures; Phylogenetic analysis; Protein evolution; Homology modeling; Protein-protein docking; Molecular dynamics simulations

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Khadka, B. (2019). Structural and Functional Aspects of Evolutionarily Conserved Signature Indels in Protein Sequences. (Doctoral Dissertation). McMaster University. Retrieved from http://hdl.handle.net/11375/25115

Chicago Manual of Style (16^th Edition):

Khadka, Bijendra. “Structural and Functional Aspects of Evolutionarily Conserved Signature Indels in Protein Sequences.” 2019. Doctoral Dissertation, McMaster University. Accessed March 05, 2021. http://hdl.handle.net/11375/25115.

MLA Handbook (7^th Edition):

Khadka, Bijendra. “Structural and Functional Aspects of Evolutionarily Conserved Signature Indels in Protein Sequences.” 2019. Web. 05 Mar 2021.

Vancouver:

Khadka B. Structural and Functional Aspects of Evolutionarily Conserved Signature Indels in Protein Sequences. [Internet] [Doctoral dissertation]. McMaster University; 2019. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/11375/25115.

Council of Science Editors:

Khadka B. Structural and Functional Aspects of Evolutionarily Conserved Signature Indels in Protein Sequences. [Doctoral Dissertation]. McMaster University; 2019. Available from: http://hdl.handle.net/11375/25115

Penn State University

10. Fan, Mengran. Accelerate the docking application on heterogeneous computing system.

Degree: 2020, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/17536mxf97

► With the recent development of structural biology, the bottlenecks of drug discovery have changed from the limited number of known protein structures to finding the… (more)

▼ With the recent development of structural biology, the bottlenecks of drug discovery have changed from the limited number of known protein structures to finding the stable docked molecular for the target proteins. Compared to directly adopt molecular docking chemical experiments, computational molecular docking offers a lower cost and less time-consuming method. However, due to the sequential algorithm designs and large memory consumption problem, most of the computational molecular docking applications are not implemented with the high-performance computing techniques, thus not fully take the benefits of computer cluster and graphics processing unit (GPU) architecture. In this thesis, we proposed a generalized molecular docking parallel strategy for Message Passing Interface (MPI) and GPU accelerating. Specifically, We maintain fault-tolerant and loading balance inside the MPI version. The GPU version carefully optimizes the main time-consuming parts targeting GPU architecture, including the reduction part, energy calculation, and memory access part. To evaluate the effectiveness of the proposed strategy, we select MedusaDock, one of the most famous computational molecular docking software, as an example to accelerate molecular docking processes. For original version MedusaDock, the docking process typically takes around a week to process one iteration on the PDBBind dataset with nearly 3900 protein-ligand pairs. Even worse, only a small portion of the protein-ligand pairs can find their docked orientation and more pairs still need much more iterations to get converge. By applying the parallel strategy on MedusaDock, our experiment result shows that both MPI and GPU version MedusaDock achieve superior performances than the original MedusaDock. The MPI version MedusaDock running on 9 nodes with 20 processes is 83.9x times faster than the original MedusaDock. If running on multiple nodes on the cluster the total time consumption can correspond reduced depending on the node number. The GPU version achieves around 1.8x times improvement on overall performance. Advisors/Committee Members: Mahmut Taylan Kandemir, Thesis Advisor/Co-Advisor, Kamesh Madduri, Thesis Advisor/Co-Advisor, Mehrdad Mahdavi, Committee Member, Chitaranjan Das, Program Head/Chair.

Subjects/Keywords: GPU architecture; Molecular docking

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Fan, M. (2020). Accelerate the docking application on heterogeneous computing system. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/17536mxf97

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Fan, Mengran. “Accelerate the docking application on heterogeneous computing system.” 2020. Thesis, Penn State University. Accessed March 05, 2021. https://submit-etda.libraries.psu.edu/catalog/17536mxf97.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Fan, Mengran. “Accelerate the docking application on heterogeneous computing system.” 2020. Web. 05 Mar 2021.

Vancouver:

Fan M. Accelerate the docking application on heterogeneous computing system. [Internet] [Thesis]. Penn State University; 2020. [cited 2021 Mar 05]. Available from: https://submit-etda.libraries.psu.edu/catalog/17536mxf97.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Fan M. Accelerate the docking application on heterogeneous computing system. [Thesis]. Penn State University; 2020. Available from: https://submit-etda.libraries.psu.edu/catalog/17536mxf97

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

11. Vrontaki, Eleni. Εικονικός βιολογικός έλεγχος βάσεων δεδομένων χημικών μορίων με τριδιάστατα μοντέλα ποσοτικών σχέσεων δομής-δράσης (3D-QSAR): εξερεύνηση καινοτόμων φαρμακευτικών μορίων για τη θεραπεία της ηπατίτιδας C και της μεσογειακής αναιμίας.

Degree: 2016, National and Kapodistrian University of Athens; Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών (ΕΚΠΑ)

URL: http://hdl.handle.net/10442/hedi/44060

► The aim of this dissertation was the in silico identification of new compoundsagainst hepatitis C and beta-thalassaemia diseases.Hepatitis C, caused by hepatitis C virus (HCV),… (more)

▼ The aim of this dissertation was the in silico identification of new compoundsagainst hepatitis C and beta-thalassaemia diseases.Hepatitis C, caused by hepatitis C virus (HCV), mainly affects the liver andhas spread worldwide in recent decades. To date, no vaccine has beendiscovered against hepatitis C virus, while the current therapy is effective onlyin limited cases. The HCV NS5B RNA-dependent RNA polymerase is the keyfunction of the replication of viral RNA, constituting a therapeutic target ofdisease. Search of inhibitors of HCV NS5B RNA polymerase has led to theinvestigation of the nucleoside (NIs) and non-nucleoside inhibitors (NNIs),targeting on the catalytic site and allosteric sites (palm, thumb, fingers) of theenzyme, respectively. NNIs have attracted the particular interest ofresearchers.Molecular docking, 3D-QSAR CoMSIA and similarity search were combined ina multi-step framework with the ultimate goal to identify potent indole analogs,in the ChEMBL database, as inhibitors of HCV replication, in a virtualscreening procedure. Initially, 41 known inhibitors were docked into theenzyme ‘‘Palm II’’ active site. In a second step, the docking pose of eachcompound was used in a receptor-based alignment for the generation of theCoMSIA fields. A validated 3D-QSAR CoMSIA model was subsequently builtto accurately estimate the activity values. The proposed framework gaveinsight into the structural characteristics that affect the binding and theinhibitory activity of these derivatives on HCV polymerase. The obtained in silico model was used to predict the activity of novel compounds prior to theirsynthesis and biological testing, within a virtual screening procedure. TheChEMBL database was mined to afford 18 compounds containing the indolescaffold that are predicted to possess high activity and thus can be prioritizedfor biological screening.A similar combination of the computational methods: (i) molecular docking, (ii)3D-QSAR CoMFA, (iii) similarity search and (iv) virtual screening usingPubChem database was applied to identify new anthranilic acid-basedinhibitors of HCV replication. 53 known inhibitors were initially docked into the ‘‘Thumb Pocket 2’’ allosteric site of the crystal structure of the RNApolymerase. Then, the CoMFA fields were generated through a receptorbasedalignment of docking poses to build a validated and stable 3D-QSARCoMFA model. The proposed model was utilized to get insight into themolecular features that promote bioactivity, and then a virtual screeningprocedure was used to estimate the activity of novel potential bioactivecompounds.Beta-thalassaemia is a common blood disorder spread worldwide, thatreduces the production of hemoglobin (Hb). Pharmacological reactivation ofthe γ-globin gene for the production of fetal haemoglobin (HbF) is a verypromising therapeutic avenue for the disease. K562 human erythroleukemiccell line has the potential to highly express the γ- but not the β-globin gene.Erythroid differentiation of K562 cells is associated with an increase in theexpression of embryo-fetal…

Subjects/Keywords: Μεσογειακή αναιμία; Μοριακή μοντελοποίηση; Μοριακή πρόσδεση; Φαρμακοφόρο μοντέλο; HCV; 3D-QSAR; CoMFA/CoMSIA; Beta-thalassaemia; Pharmacophore modeling; Molecular modeling; Molecular docking

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Vrontaki, E. (2016). Εικονικός βιολογικός έλεγχος βάσεων δεδομένων χημικών μορίων με τριδιάστατα μοντέλα ποσοτικών σχέσεων δομής-δράσης (3D-QSAR): εξερεύνηση καινοτόμων φαρμακευτικών μορίων για τη θεραπεία της ηπατίτιδας C και της μεσογειακής αναιμίας. (Thesis). National and Kapodistrian University of Athens; Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών (ΕΚΠΑ). Retrieved from http://hdl.handle.net/10442/hedi/44060

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Vrontaki, Eleni. “Εικονικός βιολογικός έλεγχος βάσεων δεδομένων χημικών μορίων με τριδιάστατα μοντέλα ποσοτικών σχέσεων δομής-δράσης (3D-QSAR): εξερεύνηση καινοτόμων φαρμακευτικών μορίων για τη θεραπεία της ηπατίτιδας C και της μεσογειακής αναιμίας.” 2016. Thesis, National and Kapodistrian University of Athens; Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών (ΕΚΠΑ). Accessed March 05, 2021. http://hdl.handle.net/10442/hedi/44060.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Vrontaki, Eleni. “Εικονικός βιολογικός έλεγχος βάσεων δεδομένων χημικών μορίων με τριδιάστατα μοντέλα ποσοτικών σχέσεων δομής-δράσης (3D-QSAR): εξερεύνηση καινοτόμων φαρμακευτικών μορίων για τη θεραπεία της ηπατίτιδας C και της μεσογειακής αναιμίας.” 2016. Web. 05 Mar 2021.

Vancouver:

Vrontaki E. Εικονικός βιολογικός έλεγχος βάσεων δεδομένων χημικών μορίων με τριδιάστατα μοντέλα ποσοτικών σχέσεων δομής-δράσης (3D-QSAR): εξερεύνηση καινοτόμων φαρμακευτικών μορίων για τη θεραπεία της ηπατίτιδας C και της μεσογειακής αναιμίας. [Internet] [Thesis]. National and Kapodistrian University of Athens; Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών (ΕΚΠΑ); 2016. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/10442/hedi/44060.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Vrontaki E. Εικονικός βιολογικός έλεγχος βάσεων δεδομένων χημικών μορίων με τριδιάστατα μοντέλα ποσοτικών σχέσεων δομής-δράσης (3D-QSAR): εξερεύνηση καινοτόμων φαρμακευτικών μορίων για τη θεραπεία της ηπατίτιδας C και της μεσογειακής αναιμίας. [Thesis]. National and Kapodistrian University of Athens; Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών (ΕΚΠΑ); 2016. Available from: http://hdl.handle.net/10442/hedi/44060

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

12. Touzeau, Jérémy. Modélisation multi-échelle de biomatériaux pour des problématiques expérimentales : Multi-scale modeling of biomaterials to solve experimental issues.

Degree: Docteur es, Chimie. Chimie Théorique et Modélisation, 2018, Sorbonne Paris Cité

URL: http://www.theses.fr/2018USPCC220

►

La confection de dispositifs impliquant des biomolécules, notamment dans le cadre de la détection (biocapteurs) ou de la protection contre des pathogènes (revêtements antimicrobiens), compte… (more)

▼

La confection de dispositifs impliquant des biomolécules, notamment dans le cadre de la détection (biocapteurs) ou de la protection contre des pathogènes (revêtements antimicrobiens), compte toujours un grand nombre d’interrogations notamment à l’échelle atomique. Dans ce contexte, nous avons utilisé les outils de la modélisation moléculaire afin de réaliser des études multi-échelles (à la fois en quantique et en mécanique moléculaire) pour étudier des systèmes (expérimentaux) impliquant des biomolécules et solutionner des problématiques. L’étude a été menée au sein de deux projets. Dans le cadre du premier d’entre eux, nous nous sommes tout d’abord intéressé à l’optimisation d’un biocapteur impliquant un transistor à effet de champ de type EGOFET, en nous concentrant plus particulièrement sur le canal semi-conducteur du transistor. Dans un second temps, nous avons réalisé une étude autour de l’interaction biologique et spécifique du biocapteur. Dans le cadre du second projet, nous nous sommes intéressés à un revêtement antimicrobien. Celui-ci s’appuie sur le greffage d’un peptide comportant une séquence d’accroche, une séquence antimicrobienne ainsi qu’un site clivable par une enzyme spécifique au pathogène que l’on souhaite traiter. En présence de ce dernier uniquement, le peptide antimicrobien est ainsi libéré dans le milieu. Bien que ce système fonctionne parfaitement en solution, ses propriétés bactéricides sont perdues lorsqu’il est greffé sur une surface, une étape indispensable pour une utilisation dans le domaine biomédicale. Nous avons ainsi étudié ce système grâce à la modélisation moléculaire afin de comprendre la perte de ces propriétés.

The tailoring of devices involving biomolecules, for applications such as the detection (biosensors) or protection against pathogens (antimicrobial coats), still introduce several interrogations at an atomic point of view. In this context, we used molecular modelling tools in order to realize multi-scale studies (quantic level and molecular mechanics level) about experimental systems and solve issues. We interested in two projects. In the first one, we firstly focused on biosensor involving filed effect transistor (EGOFET type), by studying the optimization of the semi-conductor channel. Then we interested in the specific biological interaction of the biosensor. In the second one, we interested in an antimicrobial coat. This device is composed by a peptide containing three parts: an anchoring one, a cleavable one which can be cut specifically by a surface protease of the target and so, release the last peptide in the area which involves antimicrobial properties. The system is very efficient in solution but when it’s grafted on a surface, antimicrobial properties disappear. Consequently, we used molecular modelling tools in order to prospect those antimicrobial properties loss.

Advisors/Committee Members: Barbault, Florent (thesis director), Seydou, Mahamadou (thesis director).

Subjects/Keywords: Modélisation Moléculaire; Biocapteurs; Revêtements Antimicrobiens; Dynamique Moléculaire; Docking; Multi-échelle; Modélisation quantique; Molecular Modeling; Biosensors; Antimicrobial coating; Molecular Dynamics; Molecular Docking; Multi-scale; Quantum mechanic

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Touzeau, J. (2018). Modélisation multi-échelle de biomatériaux pour des problématiques expérimentales : Multi-scale modeling of biomaterials to solve experimental issues. (Doctoral Dissertation). Sorbonne Paris Cité. Retrieved from http://www.theses.fr/2018USPCC220

Chicago Manual of Style (16^th Edition):

Touzeau, Jérémy. “Modélisation multi-échelle de biomatériaux pour des problématiques expérimentales : Multi-scale modeling of biomaterials to solve experimental issues.” 2018. Doctoral Dissertation, Sorbonne Paris Cité. Accessed March 05, 2021. http://www.theses.fr/2018USPCC220.

MLA Handbook (7^th Edition):

Touzeau, Jérémy. “Modélisation multi-échelle de biomatériaux pour des problématiques expérimentales : Multi-scale modeling of biomaterials to solve experimental issues.” 2018. Web. 05 Mar 2021.

Vancouver:

Touzeau J. Modélisation multi-échelle de biomatériaux pour des problématiques expérimentales : Multi-scale modeling of biomaterials to solve experimental issues. [Internet] [Doctoral dissertation]. Sorbonne Paris Cité; 2018. [cited 2021 Mar 05]. Available from: http://www.theses.fr/2018USPCC220.

Council of Science Editors:

Touzeau J. Modélisation multi-échelle de biomatériaux pour des problématiques expérimentales : Multi-scale modeling of biomaterials to solve experimental issues. [Doctoral Dissertation]. Sorbonne Paris Cité; 2018. Available from: http://www.theses.fr/2018USPCC220

13. Asmat, Fahmeena. Molecular recognition: preparation and identification of inclusion compounds of pharmaceutical with cyclodextrin;.

Degree: Chemistry, 2007, Aligarh Muslim University

URL: http://shodhganga.inflibnet.ac.in/handle/10603/53953

Abstract available newline newline

Bibliography p. 156-169

Advisors/Committee Members: Ali, Syed Mashhood.

Subjects/Keywords: Molecular Recognition; Preparation; Identification; Inclusion Compounds; Pharmaceutical; Cyclodextrin

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Asmat, F. (2007). Molecular recognition: preparation and identification of inclusion compounds of pharmaceutical with cyclodextrin;. (Thesis). Aligarh Muslim University. Retrieved from http://shodhganga.inflibnet.ac.in/handle/10603/53953

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Asmat, Fahmeena. “Molecular recognition: preparation and identification of inclusion compounds of pharmaceutical with cyclodextrin;.” 2007. Thesis, Aligarh Muslim University. Accessed March 05, 2021. http://shodhganga.inflibnet.ac.in/handle/10603/53953.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Asmat, Fahmeena. “Molecular recognition: preparation and identification of inclusion compounds of pharmaceutical with cyclodextrin;.” 2007. Web. 05 Mar 2021.

Vancouver:

Asmat F. Molecular recognition: preparation and identification of inclusion compounds of pharmaceutical with cyclodextrin;. [Internet] [Thesis]. Aligarh Muslim University; 2007. [cited 2021 Mar 05]. Available from: http://shodhganga.inflibnet.ac.in/handle/10603/53953.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Asmat F. Molecular recognition: preparation and identification of inclusion compounds of pharmaceutical with cyclodextrin;. [Thesis]. Aligarh Muslim University; 2007. Available from: http://shodhganga.inflibnet.ac.in/handle/10603/53953

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Vanderbilt University

14. Fu, Darwin Yu. Improving Protein-Small Molecule Structure Predictions with Ensemble Methods, or Using Computers to Guess How Tiny Things Fit Together.

Degree: PhD, Chemistry, 2018, Vanderbilt University

URL: http://hdl.handle.net/1803/13786

► Protein-small molecule structure prediction, or protein-ligand docking, is a computational method for modeling how binding partners will interaction on an atomic level. Accurate prediction of… (more)

Subjects/Keywords: Rosetta; Protein-Ligand Docking; Molecular Modeling; Small Molecules; G-Protein Coupled Receptors; Protein Structure Prediction

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Fu, D. Y. (2018). Improving Protein-Small Molecule Structure Predictions with Ensemble Methods, or Using Computers to Guess How Tiny Things Fit Together. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/13786

Chicago Manual of Style (16^th Edition):

Fu, Darwin Yu. “Improving Protein-Small Molecule Structure Predictions with Ensemble Methods, or Using Computers to Guess How Tiny Things Fit Together.” 2018. Doctoral Dissertation, Vanderbilt University. Accessed March 05, 2021. http://hdl.handle.net/1803/13786.

MLA Handbook (7^th Edition):

Fu, Darwin Yu. “Improving Protein-Small Molecule Structure Predictions with Ensemble Methods, or Using Computers to Guess How Tiny Things Fit Together.” 2018. Web. 05 Mar 2021.

Vancouver:

Fu DY. Improving Protein-Small Molecule Structure Predictions with Ensemble Methods, or Using Computers to Guess How Tiny Things Fit Together. [Internet] [Doctoral dissertation]. Vanderbilt University; 2018. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/1803/13786.

Council of Science Editors:

Fu DY. Improving Protein-Small Molecule Structure Predictions with Ensemble Methods, or Using Computers to Guess How Tiny Things Fit Together. [Doctoral Dissertation]. Vanderbilt University; 2018. Available from: http://hdl.handle.net/1803/13786

McMaster University

15. Garden, Daniel. THEORETICAL STUDY OF STATE-DEPENDENT ACTION OF TOXINS AND DRUGS IN A VOLTAGE GATED SODIUM CHANNEL.

Degree: PhD, 2011, McMaster University

URL: http://hdl.handle.net/11375/10083

► Ion permeation through voltage gated sodium channels is modulated by many drugs and toxins. However, the atomistic mechanisms of action of most these ligands… (more)

▼ Ion permeation through voltage gated sodium channels is modulated by many drugs and toxins. However, the atomistic mechanisms of action of most these ligands are poorly understood. This study focuses on three compounds: a steroidal alkaloid batrachotoxin (BTX), a pyrethroid insecticide deltamethrin, and an alkylamide insecticide BTG 502, which bind to distinct but allosterically coupled receptor sites. BTX belongs to the class of the sodium channel agonists (activators), which cause persistent channel activation by inhibiting channel inactivation. Traditionally, BTX is believed to bind at the channel-lipid interface and allosterically modulate ion permeation through the channel. However, in the last decade, amino acid residues that affect BTX action have been found in the pore-facing inner helices of all four domains, suggesting that BTX binds in the channel pore (Tikhonov and Zhorov, FEBS Letters 2005). An alkylamide insecticide BTG 502 reduces sodium currents and antagonizes the action of BTX on cockroach sodium channels, suggesting that it also binds inside the pore. Conversely, pyrethroids bind at the lipid-exposed cavity formed by a short intracellular linker-helix IIS4-S5 and transmembrane helices IIS5 and IIIS6. In this study we first developed a new method of electrostatic-energy calculations, a new protocol of ligand docking, and tested this methodology on 60 ligand-protein complexes of known structure (Garden and Zhorov 2010). We then applied this methodology to rationalize effects of various mutations in the domain III inner helix of the cockroach sodium channel BgNav1.1 on the action of BTX, BTG 502 and deltamethrin. Our collaborators, Dr. Ke Dong et al. from Michigan State University, mutated all residues in the pore-lining helix of domain III (IIIS6) and found several new BTX and BTG 502 sensing residues. Using these data along with other published data on BTX- and deltamethrin-sensing residues as distance constrains, we docked BTX, BTG 502 and deltamethrin in a Kv1.2-based homology model of the open BgNav1.1 channel. We arrived at models, which are consistent with all currently available data on the action of the ligands. In the BTX-binding model, the toxin adopts a “horseshoe” conformation and binds in the channel pore with the horseshoe plane normal to the pore axis. In this binding mode BTX allows would allow ion permeation through the hydrophilic inner face of the horseshoe, and resist the activation-gate closure. Various BTX moieties interact with known BTX sensing residues. In particular, the tertiary ammonium group of BTX is engaged in cation-p interactions with the newly discovered BTX-sensing residue Phe³ⁱ¹⁶. In the BTG 502-binding model, the ligand wraps around IIIS6 making direct contacts with all known BTG 502-sending residues, including buried residues on the IIIS6 helix side, which does not face the pore. Deltamethrin binds within the cavity formed by the linker-helix IIS4-S5, the outer helix IIS5, and the inner helix IIIS6 at the interface between domains II… Advisors/Committee Members: Zhorov, Boris, Biochemistry.

Subjects/Keywords: Ion Channels; Molecular Modeling; Drug Docking; Monte Carlo Minimization; Biochemistry; Biophysics; Biotechnology; Structural Biology; Biochemistry

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Garden, D. (2011). THEORETICAL STUDY OF STATE-DEPENDENT ACTION OF TOXINS AND DRUGS IN A VOLTAGE GATED SODIUM CHANNEL. (Doctoral Dissertation). McMaster University. Retrieved from http://hdl.handle.net/11375/10083

Chicago Manual of Style (16^th Edition):

Garden, Daniel. “THEORETICAL STUDY OF STATE-DEPENDENT ACTION OF TOXINS AND DRUGS IN A VOLTAGE GATED SODIUM CHANNEL.” 2011. Doctoral Dissertation, McMaster University. Accessed March 05, 2021. http://hdl.handle.net/11375/10083.

MLA Handbook (7^th Edition):

Garden, Daniel. “THEORETICAL STUDY OF STATE-DEPENDENT ACTION OF TOXINS AND DRUGS IN A VOLTAGE GATED SODIUM CHANNEL.” 2011. Web. 05 Mar 2021.

Vancouver:

Garden D. THEORETICAL STUDY OF STATE-DEPENDENT ACTION OF TOXINS AND DRUGS IN A VOLTAGE GATED SODIUM CHANNEL. [Internet] [Doctoral dissertation]. McMaster University; 2011. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/11375/10083.

Council of Science Editors:

Garden D. THEORETICAL STUDY OF STATE-DEPENDENT ACTION OF TOXINS AND DRUGS IN A VOLTAGE GATED SODIUM CHANNEL. [Doctoral Dissertation]. McMaster University; 2011. Available from: http://hdl.handle.net/11375/10083

16. Wallach, Izhar. Improving Posing and Ranking of Molecular Docking.

Degree: 2012, University of Toronto

URL: http://hdl.handle.net/1807/34955

►

Molecular docking is a computational tool commonly applied in drug discovery projects and fundamental biological studies of protein-ligand interactions. Traditionally, molecular docking is used to… (more)

▼

Molecular docking is a computational tool commonly applied in drug discovery projects and fundamental biological studies of protein-ligand interactions. Traditionally, molecular docking is used to address one of three following questions: (i) given a ligand molecule and a protein receptor, predict the binding mode (pose) of the ligand within the context of a receptor, (ii) screen a collection of small-molecules against a receptor and rank ligands by their likelihood of being active, and (iii) given a ligand molecule and a target receptor, predict the binding affinity of the two. Here, we focus on the first two questions, namely ranking and pose prediction. Currently, state-of-the-art docking algorithms predict poses within 2A of the native pose in a rate lower than ∼60% and in many cases, below 40%. In ranking, their ability to identify active ligands is inconsistent and generally suffers from high false-positive rate. In this thesis we present novel algorithms to enhance the ability of molecular docking to address these two questions. These algorithms do not substitute traditional docking but rather being applied on top of them to provide synergistic effect. Our algorithms improve pose predictions by 0.5-1.0A and ranking order for 23% of the targets in gold-standard benchmarks. As importantly, the algorithms improve the consistence of the posing and ranking predictions over diverse sets of targets and screening libraries. In addition to the posing and ranking, we present the pharmacophore concept. A pharmacophore is an ensemble of physiochemical descriptors associated with a biological target that elucidates common interaction patterns of ligands with that target. We introduce a novel pharmacophore inference algorithm and demonstrate its utilization in molecular docking. This thesis is outlined as follow. First we introduce the molecular docking approach for pose prediction and ranking. Second, we discuss the pharmacophore concept and present algorithms for pharmacophore inference. Third, we demonstrate the utilization of pharmacophores for pose prediction by re-scoring candidate poses generated by docking algorithms. Finally, we present algorithms to improve ranking by reducing bias in scoring functions employed by docking algorithms.

PhD

Advisors/Committee Members: Lilien, Ryan, Computer Science.

Subjects/Keywords: Docking; Molecular Modeling; Pharmacophore; 0984

…molecular weight of ∼450 Dalton. Docking was performed using eHiTS and virtual decoys were… …Chapter 4 was published as: • Virtual Decoy Sets for Molecular Docking Benchmarks, Izhar Wallach… …Normalizing Molecular Docking Rankings using Virtually Generated Decoys, Izhar Wallach, Navdeep… …1 Introduction to Molecular Docking 1.1 Introduction Molecular docking is a… …protein-ligand interactions. Traditionally, molecular docking is used to address one of the…

3 more images…

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Wallach, I. (2012). Improving Posing and Ranking of Molecular Docking. (Doctoral Dissertation). University of Toronto. Retrieved from http://hdl.handle.net/1807/34955

Chicago Manual of Style (16^th Edition):

Wallach, Izhar. “Improving Posing and Ranking of Molecular Docking.” 2012. Doctoral Dissertation, University of Toronto. Accessed March 05, 2021. http://hdl.handle.net/1807/34955.

MLA Handbook (7^th Edition):

Wallach, Izhar. “Improving Posing and Ranking of Molecular Docking.” 2012. Web. 05 Mar 2021.

Vancouver:

Wallach I. Improving Posing and Ranking of Molecular Docking. [Internet] [Doctoral dissertation]. University of Toronto; 2012. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/1807/34955.

Council of Science Editors:

Wallach I. Improving Posing and Ranking of Molecular Docking. [Doctoral Dissertation]. University of Toronto; 2012. Available from: http://hdl.handle.net/1807/34955

17. Melim, Lorane Izabel da Silva. Estudo das interações entre fosfolipases A2 e o inibidor vegetal, ácido rosmarínico de Cordia verbenacea (Boraginaceae) por cocristalização e modelagem molecular.

Degree: PhD, Toxicologia, 2009, University of São Paulo

URL: http://www.teses.usp.br/teses/disponiveis/60/60134/tde-29122009-104344/ ;

►

As peçonhas de serpente do gênero Bothrops se caracterizam por induzir miotoxicidade, edema, coagulação e hemorragia. Por essa razão, alguns pesquisadores estão buscando por tratamentos… (more)

▼

As peçonhas de serpente do gênero Bothrops se caracterizam por induzir miotoxicidade, edema, coagulação e hemorragia. Por essa razão, alguns pesquisadores estão buscando por tratamentos alternativos contra os envenenamentos ofídicos com inibidores naturais e artificiais. O presente estudo tem como objetivo estudar as interações entre as PLA2s (Asp49 e Lys49) de veneno de serpente Bothrops jararacussu, denominadas BthTX-I e BthTX-II, respectivamente, e o inibidor vegetal isolado da espécie Cordia verbenacea. C. verbenacea apresenta diversas atividades farmacológicas já demonstradas, sendo utilizada também pela população como antiofídica. O extrato hidroalcoólico das folhas preparado à seco, foi submetido a técnicas cromatográficas como Sephadex LH-20 e CLAE, obtendo-se a purificação do princípio ativo antiofídico da planta, denominado ácido rosmarínico. A peçonha de B. jararacussu foi submetida à cromatografia de filtração em gel Sephadex G-75 e, à cromatografia de troca iônica. O ácido rosmarínico (AR) foi isolado do extrato metanólico de C. verbenacea e apresentou inibição da hemorragia provocada pela peçonha bruta de B. jararacussu. Em comparação, o ácido rosmarínico® também inibiu o efeito hemorrágico causado pela peçonha bruta de B. jararacussu. A atividade edematogênica provocada pelas toxinas BthTX-I e II foi avaliada e testada com os inibidores. Ambos AR e AR® não inibiram significativamente a induçào de edema. Resultados semelhantes foram obtidos com as atividades anticoagulante, e fosfolipásica. O ácido rosmarínico, AR e AR®, demonstrou alto efeito inibitório sobre a citotoxicidade e miotoxicidade induzida pela peçonha bruta e pela toxina BthTX-I. Ambos inibidores apresentou um menor efeito sobre a atividade miotóxica induzida pela toxina BthTX-II. Simulações de docking realizadas com três PLA2s e AR mostraram perfis de interações similares, reforçando as principais interações enzima-inibidor obtidas experimentalmente, relatadas na literatura. Os cálculos de derivação de farmacóforo baseados em diferentes inibidores relatados na literatura, assim como estudos de campos de interação molecular foram realizados, nos quais os resultados indicaram as principais modificações na estrutura do inibidor ácido rosmarínico necessárias para otimização. Nas simulações de screening virtual, novos potenciais inibidores de BthTX-I foram selecionados a partir de base de dados de compostos drug-like, direcionando os próximos passos aos testes biológicos, os quais serão realizados com esta fosfolipase e os novos candidatos a inibidores modelados.

Snake venoms from Bothrops genus are characterized by inducing myotoxicity, edema, thrombosis and hemorrhage. Thus, some researchers are searching for alternative treatments against ophidian poisoning with natural and artificial inhibitors. This work aimed study the interactions between PLA2s (Asp49 e Lys49) from Bothrops jararacussu snake venom, named BthTX-I and BthTX-II, respectively, and the inhibitor isolated from Cordia verbenacea plant. C. verbenacea presents several…

Advisors/Committee Members: Silva, Carlos Henrique Tomich de Paula da, Vilela, Suely.

Subjects/Keywords: Bothrops jararacussu; Bothrops jararacussu; docking.; docking.; Inibidores de fosfolipase A2; modelagem molecular; molecular modeling; peçonha de serpente; Phospholipase A2 inhibitors; Snake venom

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Melim, L. I. d. S. (2009). Estudo das interações entre fosfolipases A2 e o inibidor vegetal, ácido rosmarínico de Cordia verbenacea (Boraginaceae) por cocristalização e modelagem molecular. (Doctoral Dissertation). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/60/60134/tde-29122009-104344/ ;

Chicago Manual of Style (16^th Edition):

Melim, Lorane Izabel da Silva. “Estudo das interações entre fosfolipases A2 e o inibidor vegetal, ácido rosmarínico de Cordia verbenacea (Boraginaceae) por cocristalização e modelagem molecular.” 2009. Doctoral Dissertation, University of São Paulo. Accessed March 05, 2021. http://www.teses.usp.br/teses/disponiveis/60/60134/tde-29122009-104344/ ;.

MLA Handbook (7^th Edition):

Melim, Lorane Izabel da Silva. “Estudo das interações entre fosfolipases A2 e o inibidor vegetal, ácido rosmarínico de Cordia verbenacea (Boraginaceae) por cocristalização e modelagem molecular.” 2009. Web. 05 Mar 2021.

Vancouver:

Melim LIdS. Estudo das interações entre fosfolipases A2 e o inibidor vegetal, ácido rosmarínico de Cordia verbenacea (Boraginaceae) por cocristalização e modelagem molecular. [Internet] [Doctoral dissertation]. University of São Paulo; 2009. [cited 2021 Mar 05]. Available from: http://www.teses.usp.br/teses/disponiveis/60/60134/tde-29122009-104344/ ;.

Council of Science Editors:

Melim LIdS. Estudo das interações entre fosfolipases A2 e o inibidor vegetal, ácido rosmarínico de Cordia verbenacea (Boraginaceae) por cocristalização e modelagem molecular. [Doctoral Dissertation]. University of São Paulo; 2009. Available from: http://www.teses.usp.br/teses/disponiveis/60/60134/tde-29122009-104344/ ;

18. Vital, Drielli Gomes. Planejamento, síntese e avaliação biológica de análogos bioisostéricos da nitrofurazona: variações de anéis (pirrol e 4-dimetilaminobenzil) e cadeias laterais (semicarbazona, tiossemicarbazona e aminoguanidina).

Degree: Mestrado, Insumos Farmacêuticos, 2013, University of São Paulo

URL: http://www.teses.usp.br/teses/disponiveis/9/9138/tde-27022014-104638/ ;

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A doença de Chagas é uma infecção causada pelo protozoário intracelular Trypanosoma cruzi. Atualmente 7 a 8 milhões de pessoas encontram-se infectadas, e há 25… (more)

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A doença de Chagas é uma infecção causada pelo protozoário intracelular Trypanosoma cruzi. Atualmente 7 a 8 milhões de pessoas encontram-se infectadas, e há 25 milhões de pessoas em áreas de risco de contaminação. A cada ano ocorrem 56.000 novos casos e, aproximadamente, 12.000 mortes por complicações oriundas da doença. É endêmica em 21 países da América do Sul, e pode ser encontrada, também, na América do Norte e Europa devido a processos migratórios. Somente dois fármacos estão disponíveis para o tratamento da doença de Chagas, o nifurtimox e o benznidazol, que são ativos somente na fase aguda e causam sérios efeitos adversos. Diante deste panorama, é eminente a necessidade de novos antichagásicos. A enzima cruzaína é a principal cisteíno-protease presente no T. cruzi, é importante para a sobrevivência, diferenciação e entrada do parasita no hospedeiro, se apresentando como um excelente alvo biológico na busca de novos quimioterápicos. Derivados de semicarbazona, tais como o nitrofural e o hidroximetilnitrofural demonstraram atividade inibitória da cruzaína, sendo considerados protótipos na busca de antichagásicos. Utilizando estratégias modernas de planejamento de fármacos por meio da integração entre técnicas computacionais, modelagem molecular e docking, e experimentais, síntese e ensaios biológicos, realizou-se neste trabalho o planejamento, síntese e avaliação biológica de bioisósteros do nitrofural como candidatos à antichagásicos. Aplicou-se estudos de modelagem molecular e docking para 10 compostos derivados de aminoguanidina, semi e tiossemicarbazona; observamos nesses estudos que os compostos contendo tiossemicarbazona apresentaram resultados mais favoráveis ao mecanismo de ação proposto, o qual sugere-se um ataque nucleofílico do resíduo de Cys25 presente no sítio catalítico da enzima cruzaína à tiocarbonila presente nesses compostos. Obtiveram-se através da síntese, 6 compostos caracterizados por RMN 1H e 13C. Tais compostos foram submetidos a ensaios de inibição da cruzaína, sendo que os derivados 6, 9 e 10, apresentaram um perfil de inibição favorável em dose de 100 µM, com valores entre 70 e 75% de inibição. Em ensaio de inibição de crescimento celular em formas epimastigotas do T. cruzi o composto 9 apresentou um IC50 de 19,8 µM, sendo o melhor protótipo para desenvolvimento de um novo agente antichagásico. De uma maneira geral os resultados obtidos nos ensaios biológicos corroboram com os dados apresentados na modelagem molecular, uma vez que os compostos contendo a cadeia lateral tiossemicarbazona mostraram melhores resultados em ambos os testes, demonstrando que a integração entre técnicas computacionais e experimentais se apresenta como uma excelente estratégia na busca de novos agentes antichagásicos.

Chagas disease is an infection caused by the intracellular protozoan Trypanosoma cruzi. Currently 7 million to 8 million people are infected, and there are 25 million people in areas at risk of contamination, with 56,000 new cases each year and roughly 12,000 deaths are related to…

Advisors/Committee Members: Trossini, Gustavo Henrique Goulart.

Subjects/Keywords: Chagas disease; Cruzain; Cruzaína; Docking; Docking; Doença de Chagas; Drug design; Modelagem molecular; Molecular modeling; Planejamento de fármacos; Trypanosoma cruzi; Trypanosoma cruzi

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Vital, D. G. (2013). Planejamento, síntese e avaliação biológica de análogos bioisostéricos da nitrofurazona: variações de anéis (pirrol e 4-dimetilaminobenzil) e cadeias laterais (semicarbazona, tiossemicarbazona e aminoguanidina). (Masters Thesis). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/9/9138/tde-27022014-104638/ ;

Chicago Manual of Style (16^th Edition):

Vital, Drielli Gomes. “Planejamento, síntese e avaliação biológica de análogos bioisostéricos da nitrofurazona: variações de anéis (pirrol e 4-dimetilaminobenzil) e cadeias laterais (semicarbazona, tiossemicarbazona e aminoguanidina).” 2013. Masters Thesis, University of São Paulo. Accessed March 05, 2021. http://www.teses.usp.br/teses/disponiveis/9/9138/tde-27022014-104638/ ;.

MLA Handbook (7^th Edition):

Vital, Drielli Gomes. “Planejamento, síntese e avaliação biológica de análogos bioisostéricos da nitrofurazona: variações de anéis (pirrol e 4-dimetilaminobenzil) e cadeias laterais (semicarbazona, tiossemicarbazona e aminoguanidina).” 2013. Web. 05 Mar 2021.

Vancouver:

Vital DG. Planejamento, síntese e avaliação biológica de análogos bioisostéricos da nitrofurazona: variações de anéis (pirrol e 4-dimetilaminobenzil) e cadeias laterais (semicarbazona, tiossemicarbazona e aminoguanidina). [Internet] [Masters thesis]. University of São Paulo; 2013. [cited 2021 Mar 05]. Available from: http://www.teses.usp.br/teses/disponiveis/9/9138/tde-27022014-104638/ ;.

Council of Science Editors:

Vital DG. Planejamento, síntese e avaliação biológica de análogos bioisostéricos da nitrofurazona: variações de anéis (pirrol e 4-dimetilaminobenzil) e cadeias laterais (semicarbazona, tiossemicarbazona e aminoguanidina). [Masters Thesis]. University of São Paulo; 2013. Available from: http://www.teses.usp.br/teses/disponiveis/9/9138/tde-27022014-104638/ ;

Université de Lorraine

19. Bidouil, Christelle. Modélisation moléculaire de l'acétylation de la quercétine par des lipases : étude des interactions enzyme-substrat : Molecular Modeling of Quercetin Acetylation by Lipases : Study of Enzyme-Substrate Interactions.

Degree: Docteur es, Procédés Biotechnologiques et Alimentaires, 2012, Université de Lorraine

URL: http://www.theses.fr/2012LORR0263

►

La quercétine (QCT) est un composé polyphénolique d'origine végétale connu pour ses activités antioxydantes et ses effets bénéfiques sur la santé. Sa solubilité, sa stabilité,… (more)

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La quercétine (QCT) est un composé polyphénolique d'origine végétale connu pour ses activités antioxydantes et ses effets bénéfiques sur la santé. Sa solubilité, sa stabilité, sa biodisponibilité et ses activités biologiques peuvent être améliorées par une acylation sélective de ses groupements hydroxylés. Ce travail vise à étudier la possibilité d'une acétylation enzymatique de la QCT par la lipase B de Candida antarctica (CALB), la lipase la plus exploitée industriellement pour des estérifications régio- et énantiosélectives. Dans une perspective d'ingénierie rationnelle de l'enzyme, une démarche de modélisation moléculaire est mise en oeuvre pour mieux comprendre les interactions qui régissent le positionnement et l'orientation du substrat dans le site actif de la lipase. Dans une première partie expérimentale, l'absence d'activité d'acétylation de la CALB envers la QCT, en présence d'un excès d'acétate de vinyle, a été confirmé. Dans une seconde partie, cette inactivité de la CALB a été expliquée à l'aide de simulations de docking et de dynamique moléculaire. Elle résulte d'une orientation inappropriée du donneur d'acyle liée à la sérine catalytique et d'une proximité insuffisante des hydroxyles de la QCT vis-à-vis des résidus catalytiques. L'éloignement de la QCT de la triade catalytique est due à la rigidité de la molécule, l'étroitesse du site actif ainsi qu'à des interactions hydrophobes et électrostatiques entre le substrat et les résidus de la cavité. En revanche, cette approche de simulation moléculaire prédit un bon positionnement des deux substrats dans le site actif de la lipase de Pseudomonas cepacia (PCL), laquelle est capable d'acétyler la QCT. Dans une troisième partie, l'influence de mutations de deux résidus impliqués dans les liaisons de stabilisation hydrophobe de la QCT dans la CALB a été investiguée par simulation. La substitution d'isoleucines par des valines et des alanines conduit à une augmentation du volume de la poche catalytique et une mobilité accrue de la QCT. Mais ces mutations sont insuffisantes pour permettre un positionnement adéquat de l'acétate et de la QCT par rapport à la triade catalytique. La dernière partie focalise sur les interactions électrostatiques entre la QCT et le site actif de CALB. Les orientations du substrat dans la cavité suite à une méthylation ou une acétylation des groupements hydroxyles de la QCT sont précisées

Quercetin (QCT) is a plant-produced polyphenolic compound well-known for its antioxidant activities and beneficial health effects. Its solubility, stability, bioavailability and biological activities may be improved by a selective acylation of its hydroxyl groups. This work aims at studying the possibility of QCT enzymatic acetylation by Candida antarctica lipase B (CALB), the most industrially exploited lipase for regio- and enantioselective esterifications. In prospect of the rational enzyme design, a molecular modeling approach was implemented to understand the interactions that govern the substrate positioning and orientation in the lipase's…

Advisors/Committee Members: Engasser, Jean-Marc (thesis director), Humeau-Virot, Catherine (thesis director).

Subjects/Keywords: Quercétine; Lipase B de Candida antarctica; Acétylation; Modélisation moléculaire; Docking; Dynamique moléculaire; Quercetin; Candida antarctica Lipase B (CALB); Acetylation; Molecular modeling; Docking; Molecular Dynamics; 541.394

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Bidouil, C. (2012). Modélisation moléculaire de l'acétylation de la quercétine par des lipases : étude des interactions enzyme-substrat : Molecular Modeling of Quercetin Acetylation by Lipases : Study of Enzyme-Substrate Interactions. (Doctoral Dissertation). Université de Lorraine. Retrieved from http://www.theses.fr/2012LORR0263

Chicago Manual of Style (16^th Edition):

Bidouil, Christelle. “Modélisation moléculaire de l'acétylation de la quercétine par des lipases : étude des interactions enzyme-substrat : Molecular Modeling of Quercetin Acetylation by Lipases : Study of Enzyme-Substrate Interactions.” 2012. Doctoral Dissertation, Université de Lorraine. Accessed March 05, 2021. http://www.theses.fr/2012LORR0263.

MLA Handbook (7^th Edition):

Bidouil, Christelle. “Modélisation moléculaire de l'acétylation de la quercétine par des lipases : étude des interactions enzyme-substrat : Molecular Modeling of Quercetin Acetylation by Lipases : Study of Enzyme-Substrate Interactions.” 2012. Web. 05 Mar 2021.

Vancouver:

Bidouil C. Modélisation moléculaire de l'acétylation de la quercétine par des lipases : étude des interactions enzyme-substrat : Molecular Modeling of Quercetin Acetylation by Lipases : Study of Enzyme-Substrate Interactions. [Internet] [Doctoral dissertation]. Université de Lorraine; 2012. [cited 2021 Mar 05]. Available from: http://www.theses.fr/2012LORR0263.

Council of Science Editors:

Bidouil C. Modélisation moléculaire de l'acétylation de la quercétine par des lipases : étude des interactions enzyme-substrat : Molecular Modeling of Quercetin Acetylation by Lipases : Study of Enzyme-Substrate Interactions. [Doctoral Dissertation]. Université de Lorraine; 2012. Available from: http://www.theses.fr/2012LORR0263

20. RABELLO, Marcelo Montenegro. Comparação metodológica de abordagens in silico no estudo de moléculas antiofídicas através de sua ação em toxinas isoladas de venenos de serpentes .

Degree: 2012, Universidade Federal de Pernambuco

URL: http://repositorio.ufpe.br/handle/123456789/18486

► Este projeto pode ser resumido como uma comparação metodológica de abordagens in silico, mais precisamente de docking molecular. Foram utilizadas como alvos biológicos as fosfolipases… (more)

▼ Este projeto pode ser resumido como uma comparação metodológica de abordagens in silico, mais precisamente de docking molecular. Foram utilizadas como alvos biológicos as fosfolipases A2 (PLA2), sendo estas um grupo de toxinas presentes abundantemente em venenos de serpentes. Foram utilizadas, como ligantes (potenciais inibidores), um total de 103 moléculas conhecidas na literatura. Um banco de dados com os ligantes e alvos foi construído, agregando-se informações sobre a atividade biológica e também suas respectivas estruturas tridimensionais. Os programas AUTODOCK, AUTODOCK VINA, GOLD, DOCK, SURFLEX e PLANTS foram utilizados para gerar os resultados de docking. O programa BINANA foi utilizado na análise das interações intermoleculares presentes nos complexos ligante-receptor, obtidos como resultados dos cálculos. Os dados gerados foram analisados com métodos multivariados, como por exemplo, a Análise de Componentes Principais (PCA) e a Análise Hierárquica de Clusters (HCA). Resíduos de aminoácidos, importantes para a estabilidade do complexo ligantereceptor, também foram identificados através de uma análise detalhada dos melhores resultados. Adicionalmente, foi reportado um artigo publicado, envolvendo PLA2s, com foco especial na molécula Quercetina como inibidor dos efeitos de veneno de serpente. Foi possível identificar os programas que apresentaram menor demanda computacional na análise comparativa de seus tempos de processamento, o que pode vir a ser muito útil em futuros estudos de docking, até mesmo com um número ainda maior de ligantes e alvos que podem ser submetidos ao procedimento de docking molecular, no intuito de aumentar o banco de dados de inibidores potenciais de PLA2s. As abordagens analíticas multivariadas utilizadas foram capazes de revelar aspectos interessantes sobre as semelhanças e diferenças entre os resultados de docking obtidos. Com a aplicação destas análises, pôde-se estabelecer uma metodologia de análise para a interpretação dos resultados nas escalas visual, numérica e gráfica, através, respectivamente, da geração das imagens para visualização molecular, das análises estatísticas (multivariadas) e da elaboração dos gráficos provenientes destas análises. Este estudo foi importante para aumentar a base de conhecimento do nosso grupo de pesquisa, e da comunidade científica como um todo, a respeito dos cálculos de modelagem molecular que envolvem os métodos de docking, e certamente serão úteis em estudos futuros com PLA2s ou outros alvos farmacológicos. Advisors/Committee Members: HERNANDES, Marcelo Zaldini (advisor).

Subjects/Keywords: Antiofídico; Docking; Comparação; Modelagem Molecular; Antiophidic; Docking; Comparison; Molecular Modelling; Serpentes- veneno; Biologia molecular; Bioinformática

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

RABELLO, M. M. (2012). Comparação metodológica de abordagens in silico no estudo de moléculas antiofídicas através de sua ação em toxinas isoladas de venenos de serpentes . (Thesis). Universidade Federal de Pernambuco. Retrieved from http://repositorio.ufpe.br/handle/123456789/18486

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

RABELLO, Marcelo Montenegro. “Comparação metodológica de abordagens in silico no estudo de moléculas antiofídicas através de sua ação em toxinas isoladas de venenos de serpentes .” 2012. Thesis, Universidade Federal de Pernambuco. Accessed March 05, 2021. http://repositorio.ufpe.br/handle/123456789/18486.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

RABELLO, Marcelo Montenegro. “Comparação metodológica de abordagens in silico no estudo de moléculas antiofídicas através de sua ação em toxinas isoladas de venenos de serpentes .” 2012. Web. 05 Mar 2021.

Vancouver:

RABELLO MM. Comparação metodológica de abordagens in silico no estudo de moléculas antiofídicas através de sua ação em toxinas isoladas de venenos de serpentes . [Internet] [Thesis]. Universidade Federal de Pernambuco; 2012. [cited 2021 Mar 05]. Available from: http://repositorio.ufpe.br/handle/123456789/18486.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

RABELLO MM. Comparação metodológica de abordagens in silico no estudo de moléculas antiofídicas através de sua ação em toxinas isoladas de venenos de serpentes . [Thesis]. Universidade Federal de Pernambuco; 2012. Available from: http://repositorio.ufpe.br/handle/123456789/18486

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Indian Institute of Science

21. Rakesh, Ramachandran. Structural and Mechanistic Features of Protein Assemblies with Special Reference to Spliceosome.

Degree: PhD, Faculty of Science, 2017, Indian Institute of Science

URL: http://etd.iisc.ac.in/handle/2005/2871

► Macromolecular assemblies such as the ribosome, spliceosome, polymerases are imperative for cellular functions. The current understanding of these important machineries and many other assemblies at… (more)

▼ Macromolecular assemblies such as the ribosome, spliceosome, polymerases are imperative for cellular functions. The current understanding of these important machineries and many other assemblies at the molecular level is poor. The lack of structural data for many macromolecular assemblies further causes a bottleneck in understanding the cellular processes and the various disease manifestations. Hence, it is essential to characterize the structures and molecular architectures of these macromolecular assemblies. Though the number of 3-D structures for individual proteins structures or domains in the Protein Data Bank (PDB) is growing, the number of structures deposited for macromolecular assemblies is relatively poor. Hence, apart from the use of experimental techniques for characterizing macromolecular assembly structures, the use of computational techniques would help in supplementing the growth of macromolecular assembly structures. This thesis deals with the use of integrative approaches where computational methods are combined with experimental data to model and understand the mechanistic features of macromolecular assemblies with a special focus on a sub-complex of the spliceosome machinery. Chapter 1 of this thesis provides an introduction to protein-protein interactions and macromolecular assemblies. Further, the modelling of macromolecular assemblies using integrative methods are discussed, with a subsequent introduction to the spliceosome machinery. In chapter 2, modelling studies were performed on the proteins involved in the general amino acid control mechanism, which is triggered in yeast under amino acid starvation conditions. The proteins involved in the study were Gcn1, a ribosome binding protein and the RWD-domain containing proteins Gcn2, Yih1, Gir2 and Mtc5. From laboratory experiments it is known that in order for Gcn2 activation, an eIF2α kinase, its RWD-domain has to bind to Gcn1 and the residue Arg-2259 is important for this interaction. As the 3-D structure for the Gcn1 region containing Arg-2259 is not currently available, its 3-D structure was inferred using fold recognition and comparative modelling techniques. Further, in order to understand the Gcn2 RWD domain-Gcn1 molecular interaction, a complex structure was inferred by using a restrained protein-protein docking procedure. As the proteins, Yih1 and Gir2 are known to bind to Gcn1 using their RWD-domains, first the structures of the RWD-domain containing proteins including Mtc5 were inferred using a Gcn2 RWD domain NMR structure. Additionally, the Gcn1-Gcn2 complex was used to build a set of complexes to explain the binding of other RWD domain containing proteins Yih1, Gir2 and Mtc5. The important molecular interactions were obtained on analysing the interacting residues in these complexes. Thus, the Gcn1-Gcn2 interaction at the molecular level has been proposed for the first time. Future experiments guided by the protein-protein complex models and the proposed set of mutations should provide an understanding about the critical molecular… Advisors/Committee Members: Srinivasan, N (advisor).

Subjects/Keywords: Macromolecular Assemblies; Splicosome Machinery; Spliceosomes; Protein Assemblies; Macromolecular Assembly Structural Modeling; Cryo-Electron Microscopy; Cryo-EM Density Modeling; Human Splicing Factor SF3B Complex; Protein-Protein Docking; Cryo-EM Map; Protein-Protein Interactions; Homologous Protein Structures; Molecular Biophyiscs

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Rakesh, R. (2017). Structural and Mechanistic Features of Protein Assemblies with Special Reference to Spliceosome. (Doctoral Dissertation). Indian Institute of Science. Retrieved from http://etd.iisc.ac.in/handle/2005/2871

Chicago Manual of Style (16^th Edition):

Rakesh, Ramachandran. “Structural and Mechanistic Features of Protein Assemblies with Special Reference to Spliceosome.” 2017. Doctoral Dissertation, Indian Institute of Science. Accessed March 05, 2021. http://etd.iisc.ac.in/handle/2005/2871.

MLA Handbook (7^th Edition):

Rakesh, Ramachandran. “Structural and Mechanistic Features of Protein Assemblies with Special Reference to Spliceosome.” 2017. Web. 05 Mar 2021.

Vancouver:

Rakesh R. Structural and Mechanistic Features of Protein Assemblies with Special Reference to Spliceosome. [Internet] [Doctoral dissertation]. Indian Institute of Science; 2017. [cited 2021 Mar 05]. Available from: http://etd.iisc.ac.in/handle/2005/2871.

Council of Science Editors:

Rakesh R. Structural and Mechanistic Features of Protein Assemblies with Special Reference to Spliceosome. [Doctoral Dissertation]. Indian Institute of Science; 2017. Available from: http://etd.iisc.ac.in/handle/2005/2871

North Carolina State University

22. Agrawal, Manisha. Formation of Beta-Cyclodextrin Inclusion Complex with a Phenolic Antioxidant and its Industrial Applications in Polyethylene Film.

Degree: MS, Textile Chemistry, 2009, North Carolina State University

URL: http://www.lib.ncsu.edu/resolver/1840.16/2267

► AGRAWAL, MANISHA. Formation of [beta]-Cyclodextrin Inclusion Complex with a Phenolic Antioxidant and its Industrial Applications in Polyethylene Film. (Under the guidance of Dr. Hyun Suk… (more)

▼ AGRAWAL, MANISHA. Formation of [beta]-Cyclodextrin Inclusion Complex with a Phenolic Antioxidant and its Industrial Applications in Polyethylene Film. (Under the guidance of Dr. Hyun Suk Whang) Butylated hydroxytoluene (BHT) is a phenolic antioxidant, which is primarily used in food additives. Due to its high volatility, it can be suspected to have losses through volatilization in high temperature applications. However, there is barely any research work focused on the formation of BHT-[beta]-CD-IC. In this study, we have successfully formed the inclusion compound between BHT and [beta]-CD (BHT-[beta]-CD-IC) and characterized it using wide-angle x-ray diffraction (WAXD), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), nuclear magnetic resonance spectroscopy (NMR) and ultra violet visible spectroscopy (UV-Vis). We produced on pilot scale three sets of low density polyethylene (LDPE) films with the addition of BHT, [beta]-CD, and BHT-[beta]-CD-IC. The determination of BHT content in the films was carried out using Gas Chromatography- Mass Spectrometry (GC-MS). The results show that 44% BHT was lost from BHT-[beta]-CD-IC LDPE films while 78% BHT was lost from the BHT LDPE film. Hence, the complex proved to be more efficient in preventing loss of BHT due to encapsulation of volatile guest. In addition, microscopy studies indicate that BHT-[beta]-CD-IC LDPE film shows small aggregates uniformly distributed over a large range in the LDPE matrix. The oxidative performance of the films was studied using differential scanning calorimetry (DSC) for determining the oxidation induction time (OITtime) and oxidation induction temperature (OITtemp.). It was found that OITtemp.method is less sensitive as compared to the OITtime method. The OITtime was 35 min for the BHT-[beta]-CD-IC LDPE film as compared with 16 min and 26 min values of LDPE and BHT LDPE films, respectively. Hence, the encapsulation of BHT in the CD maximizes the efficiency and stability to thermal degradation for BHT-[beta]-CD-IC film. The viscoelastic behavior of the films was also studied using dynamic mechanical analysis (DMA). The results indicate increase in storage modulus (El) and loss modulus of the complex (Ell). Also, the maxima of tan delta (Ell/El) for LDPE films processed with BHT, [beta]-CD and BHT-[beta]-CD-IC are shifted to lower temperature. Further, a migration study of BHT from the complex using food stimulant, which is underway, will give an insight on the controlled release of active component in the film. This may open a great potential for industrial applications of CD-ICs. Advisors/Committee Members: Alan E. Tonelli, Committee Co-Chair (advisor), Hyun Suk Whang, Committee Co-Chair (advisor), Samuel M. Hudson, Committee Member (advisor), C. M. Balik, Committee Member (advisor).

Subjects/Keywords: industrial application; cyclodextrin inclusion complex; antioxidant; packaging film

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Agrawal, M. (2009). Formation of Beta-Cyclodextrin Inclusion Complex with a Phenolic Antioxidant and its Industrial Applications in Polyethylene Film. (Thesis). North Carolina State University. Retrieved from http://www.lib.ncsu.edu/resolver/1840.16/2267

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Agrawal, Manisha. “Formation of Beta-Cyclodextrin Inclusion Complex with a Phenolic Antioxidant and its Industrial Applications in Polyethylene Film.” 2009. Thesis, North Carolina State University. Accessed March 05, 2021. http://www.lib.ncsu.edu/resolver/1840.16/2267.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Agrawal, Manisha. “Formation of Beta-Cyclodextrin Inclusion Complex with a Phenolic Antioxidant and its Industrial Applications in Polyethylene Film.” 2009. Web. 05 Mar 2021.

Vancouver:

Agrawal M. Formation of Beta-Cyclodextrin Inclusion Complex with a Phenolic Antioxidant and its Industrial Applications in Polyethylene Film. [Internet] [Thesis]. North Carolina State University; 2009. [cited 2021 Mar 05]. Available from: http://www.lib.ncsu.edu/resolver/1840.16/2267.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Agrawal M. Formation of Beta-Cyclodextrin Inclusion Complex with a Phenolic Antioxidant and its Industrial Applications in Polyethylene Film. [Thesis]. North Carolina State University; 2009. Available from: http://www.lib.ncsu.edu/resolver/1840.16/2267

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Illinois – Urbana-Champaign

23. Cassidy, C. Keith. Molecular modeling and simulation of bacterial chemosensory arrays.

Degree: PhD, Physics, 2017, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/97650

► The movement of an organism in response to environmental chemical cues is known as chemotaxis. Motile bacteria use chemotaxis to navigate through their environments, enabling… (more)

▼ The movement of an organism in response to environmental chemical cues is known as chemotaxis. Motile bacteria use chemotaxis to navigate through their environments, enabling cells to efficiently locate favorable growing conditions while avoiding harmful ones. Central to this ability, bacteria posses a universally conserved sensory apparatus, known as the chemosensory array, which involves the clustering of thousands of proteins into a highly cooperative signaling network. The present dissertation will present my work using techniques in computational modeling and simulation to investigate the molecular structure and function of the bacterial chemosensory array. A brief overview of each chapter follows. Chapter 1 provides an introduction to the systems-level features of chemotaxis in the model organism Escherichia coli as well as an overview of the molecular organization and function of the chemosensory array. Chapter 2 gives an outline of the core methodologies used in my work, specifically all-atom molecular dynamics (MD) simulation and Molecular Dynamics Flexible Fitting (MDFF). In addition, two of the primary techniques used to analyze the MD simulations presented in this dissertation are sketched out, namely structural clustering based on root- mean-square displacement (RMSD) and Principal Component Analysis (PCA). Chapter 3 reports my work, in collaboration with Peijun Zhang’s Lab, to investigate the structural and dynamical features of the extended chemosensory array. Using computational techniques to synthesize multi-scale structural data from X-ray crystallography and cryo-electron tomography (cryo-ET), an atomic model of the cytoplasmic portion of the chemosensory array from Thermotoga maritima is constructed and refined. Through the use of large-scale MD simulations, a novel conformational change in a key signaling protein is identified and subsequently shown to be critical for chemotaxis signaling in live E. coli cells. Chapter 4 details the construction of an atomic model of a complete, transmembrane (TM) chemoreceptor. In particular, I use homology modeling and MD simulations, in- formed by biochemical and X-ray crystallographic data, to derive a model of the E. coli serine receptor (Tsr), including the previously uncharacterized TM four-helix bundle and HAMP domains. In addition, I report a series of MD simulations of a fragment of the resulting Tsr model, investigating the structural and dynamical effects of mutations on a key control cable residue. Preliminary MD simulations of the intact Tsr model are also presented. Chapter 5 reports work in collaboration with Michael Eisenbach’s Lab at the Weizmann Institute, exploring the role of acetylation on CheY activation and the generation of clockwise (CW) flagellar motor rotation. Specifically, I present a series of MD simulations that investigate the effect of a hyperactivating mutation at a key acetylation site and offer a molecular explanation of acetylation-dependent generation of CW flagellar motor rotation. I conclude with a brief… Advisors/Committee Members: Schulten, Klaus (advisor), Chemla, Yann R (Committee Chair), Luthey-Schulten, Zaida (committee member), Cooper, Lance S (committee member), Stack, John D (committee member).

Subjects/Keywords: Bacterial chemotaxis; Chemosensory array; Chemoreceptor; Molecular dynamics; Molecular modeling; Multi-protein complex

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Cassidy, C. K. (2017). Molecular modeling and simulation of bacterial chemosensory arrays. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/97650

Chicago Manual of Style (16^th Edition):

Cassidy, C Keith. “Molecular modeling and simulation of bacterial chemosensory arrays.” 2017. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 05, 2021. http://hdl.handle.net/2142/97650.

MLA Handbook (7^th Edition):

Cassidy, C Keith. “Molecular modeling and simulation of bacterial chemosensory arrays.” 2017. Web. 05 Mar 2021.

Vancouver:

Cassidy CK. Molecular modeling and simulation of bacterial chemosensory arrays. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2017. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2142/97650.

Council of Science Editors:

Cassidy CK. Molecular modeling and simulation of bacterial chemosensory arrays. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2017. Available from: http://hdl.handle.net/2142/97650

24. Triantafyllopoulou, Vasiliki. Ανάλυση της κρυσταλλικής δομής προϊόντων εγκλεισμού.

Degree: 2013, Agricultural University of Athens; Γεωπονικό Πανεπιστήμιο Αθηνών

URL: http://hdl.handle.net/10442/hedi/34911

► Cyclodextrins (CDs) are cyclic oligosaccharides consisting of six, seven or eight α-(1-4)-linked D-glucose residues, called respectively α-, β- or γ- CD. As they possess a… (more)

▼ Cyclodextrins (CDs) are cyclic oligosaccharides consisting of six, seven or eight α-(1-4)-linked D-glucose residues, called respectively α-, β- or γ- CD. As they possess a hydrophobic cavity, the hydrophobic moieties of a wide variety of guest molecules, having suitable size and shape, may be included there and form inclusion compounds. The guest molecules are held inside the CD cavity by non-covalent interactions, such as hydrogen bonds, van der Waals or hydrophobic interactions. The encapsulation modifies the physico-chemical properties of the guests by increasing their solubility in water and resulting in an augmented protection against chemical degradation, oxidation, etc.The structures of the inclusion compounds: 4-chloro-2-methylphenoxyacetic acid (MCPA), 2,4-dichlorophenoxyacetic acid (2,4-D) and β-naphthylacetic acid (2-NAA) in β-Cyclodextrin (β-CD) has been investigated by X-ray crystallography and their action has been tested on the bioindicators Avena sativa (oat), Vicia faba (broad beans) and Lemna minor.The inclusion complex MCPA/β-CD, crystallizes in the P21 space group. Its asymmetric unit contains two β-CD molecules hosting two disordered MCPA guest molecules (2:2 host:guest stoichiometry) occupying overall five sites. It also contains 16.13 water molecules distributed over 36 sites. One water molecule is entrapped inside the dimeric cavity, forming a hydrogen bond with the chlorine atom of a guest. The two complexes of the asymmetric unit are located alongside and they form head-to-head dimers with the symmetry related complexes by the 2-fold screw axis (b-axis). The dimers form channels developed along the a-axis.The inclusion compound of 2,4-dichlorophenoxyacetic acid in β-Cyclodextrin (2,4-D/β-CD) crystallizes in space group P1 and forms dimers installed along the c axis forming channels. A guest molecule, extended inside all over the dimeric cavity, is disorder over three sites, having an overall occupancy of 1.0 and, therefore, the host:guest stoichiometry is 2:1. 1.47 water molecules are located inside the dimeric cavity, distributed over four sites.The 2-NAA/β-CD complex crystallizes in the triclinic system forming a dimer inside the cavity of which two 2-NAA molecules, disordered over two sites, are located. The dimers are stacked along the c axis according to the channel packing mode forming a nanotube which resembles a wireway as it contains guest molecules linked by π-πinteractions inside each dimeric cavity and by H-bonds between the adjacent dimers.As concerned the orientation of the guest molecules in the 2-NAA/β-CD complex,their naphthalene moieties are accommodated deeply inside the dimeric cavity whiletheir carboxyl groups are located in the rim of their primary hydroxyl groupsprotruding from the host cavity, due to the π-π interactions between the naphthalenemoieties of the encapsulated molecules inside the dimeric cavity.Furthermore, the action of the above auxins and their inclusion compounds with β-CDhas been tested on the bioindicators Avena sativa (oat), Vicia faba (broad…

Subjects/Keywords: 4-χλωρο-2-μεθυλοφαινοξυοξικό οξύ (MCPA); 2,4-διχλωροφαινοξυοξικό οξύ (2,4D); 2-ναφθυλοξικό οξύ (2-NAA); Β-ΚΥΚΛΟΔΕΞΤΡΙΝΗ; Προϊόντα εγκλεισμού; Κρυσταλλική δομή; Βιοδοκιμές; Ανάπτυξη ριζιδίου; Αργή απελευθέρωση; Μοριακή μοντελοποίηση; Βιοδείκτες Avena sativa, Vicia faba, Lemna minor; 4-chloro-2-methylphenoxyacetic acid (MCPA); 2,4-dichlorophenoxyacetic acid (2,4D); 2-naphthylacetic acid (2-NAA); β-cyclodextrin; Inclusion complexes; Crystal structure; Bioassays; Radicle growth; Slow release; Molecular docking; Bioindicators Avena sativa, Vicia faba, Lemna minor

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Triantafyllopoulou, V. (2013). Ανάλυση της κρυσταλλικής δομής προϊόντων εγκλεισμού. (Thesis). Agricultural University of Athens; Γεωπονικό Πανεπιστήμιο Αθηνών. Retrieved from http://hdl.handle.net/10442/hedi/34911

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Triantafyllopoulou, Vasiliki. “Ανάλυση της κρυσταλλικής δομής προϊόντων εγκλεισμού.” 2013. Thesis, Agricultural University of Athens; Γεωπονικό Πανεπιστήμιο Αθηνών. Accessed March 05, 2021. http://hdl.handle.net/10442/hedi/34911.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Triantafyllopoulou, Vasiliki. “Ανάλυση της κρυσταλλικής δομής προϊόντων εγκλεισμού.” 2013. Web. 05 Mar 2021.

Vancouver:

Triantafyllopoulou V. Ανάλυση της κρυσταλλικής δομής προϊόντων εγκλεισμού. [Internet] [Thesis]. Agricultural University of Athens; Γεωπονικό Πανεπιστήμιο Αθηνών; 2013. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/10442/hedi/34911.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Triantafyllopoulou V. Ανάλυση της κρυσταλλικής δομής προϊόντων εγκλεισμού. [Thesis]. Agricultural University of Athens; Γεωπονικό Πανεπιστήμιο Αθηνών; 2013. Available from: http://hdl.handle.net/10442/hedi/34911

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

25. Koukoulitsa, Aikaterini. Σχεδιασμός καινοτόμων βιοδραστικών μορίων με τη βοήθεια της μοριακής προσομοίωσης για την αντιμετώπιση των εκφυλιστικών νόσων του Κ.Ν.Σ: alzheimer και parkinson.

Degree: 2014, National and Kapodistrian University of Athens; Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών (ΕΚΠΑ)

URL: http://hdl.handle.net/10442/hedi/42578

►

The aim of this dissertation is the in silico rational design of new compounds against Alzheimer's and Parkinson diseases.The aspartic protease BACE-1 is a therapeutic… (more)

▼

The aim of this dissertation is the in silico rational design of new compounds against Alzheimer's and Parkinson diseases.The aspartic protease BACE-1 is a therapeutic target for Alzheimer's disease. Therefore, a series of 11 resveratrol derivatives and 11 glyoxylato-aroylhydrazones were studied against BACE-1. Initially, we studied their ability to penetrate the blood brain barrier (BBB) and be absorbed by the cells of the intestine epithelium Caco2. Furthermore, molecular docking calculations were performed in the active site of BACE-1. The results were promising and the compounds were biologically evaluated against the enzyme. Resveratrol and four derivatives of resveratrol showed significant inhibitory activity. The remaining derivatives were inactive. The glyoxylato-aroylhydrazones showed no significant inhibitory activity. These derivatives were also studied for their suppress the induction of cell death due to oxidative stress of HT22 cells. The comparison of the results of these two biological tests reveals that the activity of these compounds may be dual: first act as BACE-1 inhibitors and second protect nerve cells from oxidative death. Experiments on Differential Scanning Calorimetry and Molecular Dynamics techniques showed that the most active compounds exert stronger thermal effects.One of the classes of drugs used to treat Parkinson's disease is the monoamine oxidase type B (MAO-B). Literature studies support the inhibitory activity of coumarins against MAO-B. Thus, a series of 13 coumarin derivatives was studied. Initially, we evaluated the pharmacokinetic properties of the compounds and then we applied molecular docking in the active site of MAO-B. The results from both studies are encouraging and the compounds are under biological evaluation.AT1 antagonists exert antioxidant effects and may have beneficial effects in Alzheimer’s disease. For this reason, we investigated a possible activity of the synthetic analogue BV6 against BACE-1 using molecular docking studies. The results are promising and BV6 will be shortly biologically evaluated.

Σκοπός της διδακτορικής διατριβής είναι ο in silico ορθολογικός σχεδιασμός νέων ενώσεων κατά των νόσων της Alzheimer και Parkinson.Ένας θεραπευτικός στόχος της νόσου Αlzheimer είναι η ασπαρτική πρωτεάση BACE-1. Ως προς την κατεύθυνση αναστολής της δράσης αυτού του ενζύμου μελετήθηκαν 11 παράγωγα της ρεσβερατρόλης και 11 γλυοξυλοϋλο-αροϋλο παράγωγα της υδραζόνης. Αρχικά μελετήθηκε in silico η ικανότητά τους να διαπερνούν τον αιματοεγκεφαλικό φραγμό και να απορροφώνται από τα κύτταρα του επιθηλίου του εντέρου Caco2 και ακολούθησαν υπολογισμοί μοριακής πρόσδεσης των παραγώγων δύο ομάδων στο ενεργό κέντρο της BACE-1. Επειδή τα αποτελέσματα της μοριακής πρόσδεσης ήταν ενθαρρυντικά ακολούθησε βιολογική τους αποτίμηση στη BACE-1. Πέντε παράγωγα της ρεσβερατρόλης παρουσίασαν σημαντική ανασταλτική δράση. Τα υπόλοιπα παράγωγα ήταν μη δραστικά. Τα γλυοξυλοϋλο-αροϋλο παράγωγα δεν εμφάνισαν σημαντική ανασταλτική δράση. Τα παράγωγα και των δύο ομάδων μελετήθηκαν επίσης για την…

Subjects/Keywords: Ορθολογικός σχεδιασμός; Εκτίμηση φαρμακοκινητικών ιδιοτήτων; Μοριακή μοντελοποίηση; Μοριακή πρόσδεση; Προσομοιώσεις μοριακής δυναμικής; Rational design; in silico evaluation of pharmacokinetic properties; Molecular modeling; Molecular docking; Molecular dynamics simulations

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Koukoulitsa, A. (2014). Σχεδιασμός καινοτόμων βιοδραστικών μορίων με τη βοήθεια της μοριακής προσομοίωσης για την αντιμετώπιση των εκφυλιστικών νόσων του Κ.Ν.Σ: alzheimer και parkinson. (Thesis). National and Kapodistrian University of Athens; Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών (ΕΚΠΑ). Retrieved from http://hdl.handle.net/10442/hedi/42578

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Koukoulitsa, Aikaterini. “Σχεδιασμός καινοτόμων βιοδραστικών μορίων με τη βοήθεια της μοριακής προσομοίωσης για την αντιμετώπιση των εκφυλιστικών νόσων του Κ.Ν.Σ: alzheimer και parkinson.” 2014. Thesis, National and Kapodistrian University of Athens; Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών (ΕΚΠΑ). Accessed March 05, 2021. http://hdl.handle.net/10442/hedi/42578.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Koukoulitsa, Aikaterini. “Σχεδιασμός καινοτόμων βιοδραστικών μορίων με τη βοήθεια της μοριακής προσομοίωσης για την αντιμετώπιση των εκφυλιστικών νόσων του Κ.Ν.Σ: alzheimer και parkinson.” 2014. Web. 05 Mar 2021.

Vancouver:

Koukoulitsa A. Σχεδιασμός καινοτόμων βιοδραστικών μορίων με τη βοήθεια της μοριακής προσομοίωσης για την αντιμετώπιση των εκφυλιστικών νόσων του Κ.Ν.Σ: alzheimer και parkinson. [Internet] [Thesis]. National and Kapodistrian University of Athens; Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών (ΕΚΠΑ); 2014. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/10442/hedi/42578.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Koukoulitsa A. Σχεδιασμός καινοτόμων βιοδραστικών μορίων με τη βοήθεια της μοριακής προσομοίωσης για την αντιμετώπιση των εκφυλιστικών νόσων του Κ.Ν.Σ: alzheimer και parkinson. [Thesis]. National and Kapodistrian University of Athens; Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών (ΕΚΠΑ); 2014. Available from: http://hdl.handle.net/10442/hedi/42578

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Universiteit Utrecht

26. Enckevort, C.M.W. van. Students' learning of molecular modeling. The case of computer-aided drug design against malaria disease.

Degree: 2014, Universiteit Utrecht

URL: http://dspace.library.uu.nl:8080/handle/1874/298078

► Models are important tools used in the production, dissemination and acceptance of scientific knowledge (Dori & Barak, 2001, p. 62). The skills to learn with,… (more)

Subjects/Keywords: Molecular modeling

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APA (6^th Edition):

Enckevort, C. M. W. v. (2014). Students' learning of molecular modeling. The case of computer-aided drug design against malaria disease. (Masters Thesis). Universiteit Utrecht. Retrieved from http://dspace.library.uu.nl:8080/handle/1874/298078

Chicago Manual of Style (16^th Edition):

Enckevort, C M W van. “Students' learning of molecular modeling. The case of computer-aided drug design against malaria disease.” 2014. Masters Thesis, Universiteit Utrecht. Accessed March 05, 2021. http://dspace.library.uu.nl:8080/handle/1874/298078.

MLA Handbook (7^th Edition):

Enckevort, C M W van. “Students' learning of molecular modeling. The case of computer-aided drug design against malaria disease.” 2014. Web. 05 Mar 2021.

Vancouver:

Enckevort CMWv. Students' learning of molecular modeling. The case of computer-aided drug design against malaria disease. [Internet] [Masters thesis]. Universiteit Utrecht; 2014. [cited 2021 Mar 05]. Available from: http://dspace.library.uu.nl:8080/handle/1874/298078.

Council of Science Editors:

Enckevort CMWv. Students' learning of molecular modeling. The case of computer-aided drug design against malaria disease. [Masters Thesis]. Universiteit Utrecht; 2014. Available from: http://dspace.library.uu.nl:8080/handle/1874/298078

Universidade do Minho

27. Costa, Rui Sérgio Magalhães da. Scalar algorithms for molecular docking in heterogeneous platforms .

Degree: 2011, Universidade do Minho

URL: http://hdl.handle.net/1822/27903

► The high throughput screening of new candidate drugs uses computational intensive molecular docking simulations. State-of-the art implementations for multicore-CPU systems still have performance, precision and… (more)

▼ The high throughput screening of new candidate drugs uses computational intensive molecular docking simulations. State-of-the art implementations for multicore-CPU systems still have performance, precision and accuracy limitations, which require an increase in the efficiency and scalability of both molecular docking algorithms and their coding. Current heterogenous platforms that merge multicore CPU with CUDA enabled GPU devices are an affordable accelerating technology that may overcome the performance limitations. The dissertation work aims to efficiently port to an heterogeneous platform a popular open source software package for molecular docking, Autodock Vina, keeping the functionality of the original algorithms whenever feasible. The new version, ScalaVina, predicts the noncovalent chemical interaction of a small molecule (ligand) against the binding site of a receptor macromolecule (receptor), evaluating the fitness of the ligand inside the binding pocket using a scoring function, and searching the best structural fit between ligand and receptor with the lowest local minima binding energy. The original Vina supports multithreaded parallelism at a high level, by launching multiple starting points with sequential activities, which include the global optimizer heuristic algorithm iterated local search, ILS, the energy minimization function using the BFGS algorithm, the multivariable scoring function and other support functions. The development of the ScalaVina version to take advantage of a CUDA enabled GPU required the parallelization of these functions under the SIMD paradigm, while attempting to minimize data transfers to/from the accelerating board and to improve data access patterns. Each starting point was mapped into one streaming multiprocessor at the GPU device, exploring the SIMD multithreaded parallelism to compute the values required for the docking operations above mentioned. This approach mimics the original Vina when it allocates a hardware block (SM) in the GPU for each starting point; however, these functions are executed in parallel in the GPU. Obtained results show that the GPU output of ScalaVina is in qualitative and quantitative agreement with experimental data and closely matches the output of Vina for the same set of receptor: ligand pairs. Preliminary performance results also show that there is room for improvements with careful tuning. Advisors/Committee Members: Proença, Alberto José (advisor), Micaelo, N. M (advisor).

Subjects/Keywords: GPU computing; Molecular docking; Heterogeneous computing

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APA (6^th Edition):

Costa, R. S. M. d. (2011). Scalar algorithms for molecular docking in heterogeneous platforms . (Masters Thesis). Universidade do Minho. Retrieved from http://hdl.handle.net/1822/27903

Chicago Manual of Style (16^th Edition):

Costa, Rui Sérgio Magalhães da. “Scalar algorithms for molecular docking in heterogeneous platforms .” 2011. Masters Thesis, Universidade do Minho. Accessed March 05, 2021. http://hdl.handle.net/1822/27903.

MLA Handbook (7^th Edition):

Costa, Rui Sérgio Magalhães da. “Scalar algorithms for molecular docking in heterogeneous platforms .” 2011. Web. 05 Mar 2021.

Vancouver:

Costa RSMd. Scalar algorithms for molecular docking in heterogeneous platforms . [Internet] [Masters thesis]. Universidade do Minho; 2011. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/1822/27903.

Council of Science Editors:

Costa RSMd. Scalar algorithms for molecular docking in heterogeneous platforms . [Masters Thesis]. Universidade do Minho; 2011. Available from: http://hdl.handle.net/1822/27903

Universidad de Chile

28. Buldrini Oviedo, María Teresa. Identificación de Potenciales Residuos Determinantes de Mayor Afinidad a Celulosa en una Endoglucanasa Mediante Estudios de Docking Molecular.

Degree: 2012, Universidad de Chile

URL: http://repositorio.uchile.cl/handle/2250/104415

► El bioetanol es un combustible complementario a las gasolinas, producido mediante fermentación de azúcares simples derivados de sacarosa, almidón o celulosa. Debido a su gran… (more)

▼ El bioetanol es un combustible complementario a las gasolinas, producido mediante fermentación de azúcares simples derivados de sacarosa, almidón o celulosa. Debido a su gran abundancia el material celulósico es particularmente atractivo como fuente de combustible. La hidrólisis de la celulosa puede realizase utilizando métodos químicos (ácidos o bases) o enzimáticos. La hidrólisis enzimática genera productos más puros y consume menos energía; sin embargo, debido a su bajo rendimiento se requiere usar grandes cantidades de enzima, lo cual eleva considerablemente los costos de producción. Las endoglucanasas son glicosil hidrolasas que rompen enlaces β-1,4 en polímeros de glucosa. Actúan sobre enlaces internos de la celulosa amorfa generando su despolimerización. La estructura de las celulasas incluye un módulo catalítico, unido a un dominio que actúa como centro de anclaje a la celulosa, por lo que se le ha denominado Modulo de Unión a Carbohidrato (CBM por su sigla en Inglés). Estudios previos han demostrado que una alta afinidad a celulosa se correlaciona con un aumento en la hidrólisis de ésta. En el presente trabajo se proponen mutaciones en el CBM de la endo β-1,4 glucanasa de Trametes versicolor (TvEG), que aumenten la adsorción de la enzima sobre celulosa, buscando de este modo aumentar la hidrólisis de ésta. Se generó un modelo tridimensional del CBM de la endoglucanasa de T. versicolor mediante modelación comparativa. La estructura obtenida está formada por tres hojas beta antiparalelas unidas entre sí mediante dos puentes disulfuro. El modelo generado se utilizó para llevar a cabo estudios de Docking Molecular, para identificar regiones de interacción celulosa–CBM. Usando los resultados de la simulación computacional de la interacción CBM-celulosa, se identificaron dos zonas de unión. La primera concuerda con la reportada previamente para CBM’s de la familia I, mientras que no existen reportes en la literatura sobre interacción de la celulosa con la segunda zona identificada. A continuación se simuló mediante Docking Molecular, la interacción de celulosa con variantes de CBM que contenían diferentes aminoácidos en las posiciones clave de la segunda zona de interacción; los valores de energía libre de unión entregados por la simulación permitieron sugerir tres variantes de secuencia de CBM. Las variantes seleccionadas fueron: variante 1 (G7Y, F10W), variante 2 (G7Y, F10W, G12Q) y variante 3 (G7Y, G9Q, F10W, G12Q), donde G es glicina, Y tirosina, F fenilalanina, W triptófano y Q glutamina. Se generó un sistema de expresión recombinante de TvEG mediante clonamiento del gen silvestre de la enzima en el vector pET22b(+) y transformación en E. coli BL21(DE3); la proteína se acumuló intracelularmente en forma activa. Las mutaciones planteadas fueron construidas exitosamente mediante mutagénesis sitio dirigida, utilizando la metodología de mutación por extensión de superposición. De esta forma, se deja planteado un sistema de expresión recombinante de las variantes construidas, de modo de en el futuro…

Subjects/Keywords: Biotecnología; Celulosa; Endogluconasa; Docking molecular; CMB

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Buldrini Oviedo, M. T. (2012). Identificación de Potenciales Residuos Determinantes de Mayor Afinidad a Celulosa en una Endoglucanasa Mediante Estudios de Docking Molecular. (Thesis). Universidad de Chile. Retrieved from http://repositorio.uchile.cl/handle/2250/104415

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Buldrini Oviedo, María Teresa. “Identificación de Potenciales Residuos Determinantes de Mayor Afinidad a Celulosa en una Endoglucanasa Mediante Estudios de Docking Molecular.” 2012. Thesis, Universidad de Chile. Accessed March 05, 2021. http://repositorio.uchile.cl/handle/2250/104415.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Buldrini Oviedo, María Teresa. “Identificación de Potenciales Residuos Determinantes de Mayor Afinidad a Celulosa en una Endoglucanasa Mediante Estudios de Docking Molecular.” 2012. Web. 05 Mar 2021.

Vancouver:

Buldrini Oviedo MT. Identificación de Potenciales Residuos Determinantes de Mayor Afinidad a Celulosa en una Endoglucanasa Mediante Estudios de Docking Molecular. [Internet] [Thesis]. Universidad de Chile; 2012. [cited 2021 Mar 05]. Available from: http://repositorio.uchile.cl/handle/2250/104415.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Buldrini Oviedo MT. Identificación de Potenciales Residuos Determinantes de Mayor Afinidad a Celulosa en una Endoglucanasa Mediante Estudios de Docking Molecular. [Thesis]. Universidad de Chile; 2012. Available from: http://repositorio.uchile.cl/handle/2250/104415

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

29. SILVA, Aluizio Galdino da. Estudos de QSAR e docking molecular de compostos oxadiazólicos e tiossemicarbazônicos como agentes larvicidas para o Aedes Aegypti .

Degree: 2015, Universidade Federal de Pernambuco

URL: https://repositorio.ufpe.br/handle/123456789/33187

► Neste trabalho apresentamos os resultados de um estudo teórico envolvendo as relações quantitativas estrutura-atividade (QSAR) e docking molecular para três classes de compostos possuindo atividades… (more)

Subjects/Keywords: Aedes aegypti; QSAR; Docking molecular; Atividade larvicida

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

SILVA, A. G. d. (2015). Estudos de QSAR e docking molecular de compostos oxadiazólicos e tiossemicarbazônicos como agentes larvicidas para o Aedes Aegypti . (Doctoral Dissertation). Universidade Federal de Pernambuco. Retrieved from https://repositorio.ufpe.br/handle/123456789/33187

Chicago Manual of Style (16^th Edition):

SILVA, Aluizio Galdino da. “Estudos de QSAR e docking molecular de compostos oxadiazólicos e tiossemicarbazônicos como agentes larvicidas para o Aedes Aegypti .” 2015. Doctoral Dissertation, Universidade Federal de Pernambuco. Accessed March 05, 2021. https://repositorio.ufpe.br/handle/123456789/33187.

MLA Handbook (7^th Edition):

SILVA, Aluizio Galdino da. “Estudos de QSAR e docking molecular de compostos oxadiazólicos e tiossemicarbazônicos como agentes larvicidas para o Aedes Aegypti .” 2015. Web. 05 Mar 2021.

Vancouver:

SILVA AGd. Estudos de QSAR e docking molecular de compostos oxadiazólicos e tiossemicarbazônicos como agentes larvicidas para o Aedes Aegypti . [Internet] [Doctoral dissertation]. Universidade Federal de Pernambuco; 2015. [cited 2021 Mar 05]. Available from: https://repositorio.ufpe.br/handle/123456789/33187.

Council of Science Editors:

SILVA AGd. Estudos de QSAR e docking molecular de compostos oxadiazólicos e tiossemicarbazônicos como agentes larvicidas para o Aedes Aegypti . [Doctoral Dissertation]. Universidade Federal de Pernambuco; 2015. Available from: https://repositorio.ufpe.br/handle/123456789/33187

University of New Mexico

30. Adamson, Torin. Molecular Docking With Haptic Guidance and Path Planning.

Degree: Department of Computer Science, 2016, University of New Mexico

URL: http://hdl.handle.net/1928/32227

► Molecular docking drives many important biological processes including immune system recognition and cellular signalling. Molecular docking occurs when molecules interact and form complexes. Predicting how… (more)

▼ Molecular docking drives many important biological processes including immune system recognition and cellular signalling. Molecular docking occurs when molecules interact and form complexes. Predicting how specific molecules dock with each other using computational methods has several applications including understanding diseases and virtual drug design. The goal of molecular docking prediction is to find the lowest energy ligand states. The lower the energy state, the more probable the state is docked and biologically feasible. Existing automated computational methods can be time intensive, especially when using direct molecular dynamic simulation. One way to reduce this computational cost is to use more coarse-grained models that approximate molecular docking. Coarse-grained molecular docking prediction is generally performed first by sampling ligand states using a rigid body model or a partial flexibility model to reduce computation, then by screening the states. The ligand states are screened using a scoring function, usually a potential energy function for interactions between the atoms in each molecule. Ligand state search algorithms still have a significant computational cost if a large portion of the state space is to be explored. Instead of an automated ligand state search method, a human operator can explore the state space instead. Haptic force feedback devices providing guidance based off the energy function can aid the human operator. Haptic-guidance has been used for immersive semi-automatic and manual molecular docking on a single operator scale. A large amount of ligand state space can be explored with many human operators in a crowdsourced effort. Players in an interactive crowdsourced protein folding puzzle game have aided in finding protein folding prediction solutions, but without haptic feedback. Interactive crowdsourced methods for molecular docking prediction is not well-explored, although non-interactive crowdsourced systems such as [email protected] can be adapted for molecular docking. This thesis presents a molecular docking game that produces low potential energy ligand states and motion paths with crowdsource scale potential. In an exploratory user study, participants were assigned four different types of devices with varying levels of haptic guidance to search for a potentially docked ligand state. The results demonstrate some effect on the type of device and haptic guidance seen in the study. However, differences are minimal thus potentially enabling the use of commonly available input devices in a crowdsourced setting. Advisors/Committee Members: Tapia, Lydia, Kelley, Patrick, Tapia, Lydia, Kelley, Patrick, Jacobson, Bruna, Castellanos, Joel.

Subjects/Keywords: Probabilistic Roadmap Methods; Molecular Docking; Haptics; Crowdsourcing

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Adamson, T. (2016). Molecular Docking With Haptic Guidance and Path Planning. (Masters Thesis). University of New Mexico. Retrieved from http://hdl.handle.net/1928/32227

Chicago Manual of Style (16^th Edition):

Adamson, Torin. “Molecular Docking With Haptic Guidance and Path Planning.” 2016. Masters Thesis, University of New Mexico. Accessed March 05, 2021. http://hdl.handle.net/1928/32227.

MLA Handbook (7^th Edition):

Adamson, Torin. “Molecular Docking With Haptic Guidance and Path Planning.” 2016. Web. 05 Mar 2021.

Vancouver:

Adamson T. Molecular Docking With Haptic Guidance and Path Planning. [Internet] [Masters thesis]. University of New Mexico; 2016. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/1928/32227.

Council of Science Editors:

Adamson T. Molecular Docking With Haptic Guidance and Path Planning. [Masters Thesis]. University of New Mexico; 2016. Available from: http://hdl.handle.net/1928/32227

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Open Access Theses and Dissertations