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You searched for +publisher:"San Jose State University" +contributor:("Brooke Lustig"). One record found.

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San Jose State University

1. Strauss, Benjamin. PREDICTING SWITCH-LIKE BEHAVIOR IN PROTEINS USING LOGISTIC REGRESSION ON SEQUENCE-BASED DESCRIPTORS.

Degree: MS, Computer Science, 2019, San Jose State University

Ligands can bind at specific protein locations, inducing conformational changes such as those involving secondary structure. Identifying these possible switches from sequence, including homology, is an important ongoing area of research. We attempt to predict possible secondary structure switches from sequence in proteins using machine learning, specifically a logistic regression approach with 48 N-acetyltransferases as our learning set and 5 sirtuins as our test set. Validated residue binary assignments of 0 (no change in secondary structure) and 1 (change in secondary structure) were determined (DSSP) from 3D X-ray structures for sets of virtually identical chains crystallized under different conditions. Our sequence descriptors include amino acid type, six and twenty-term sequence entropy, Lobanov-Galzitskaya’s residue disorder propensity, Vkabat (variablility with respect to predictions from sequence of helix, sheet and other), and all possible combinations. We find the optimal AUC values approaching 70% for the two models of just residue disorder propensity and separately Vkabat. We hope to follow up with a larger learning set and using residue charge as an additional descriptor. Advisors/Committee Members: Jon Pearce, Brooke Lustig, Sami Khuri.

Subjects/Keywords: secondary DNA structure switches; machine learning; regression; Numerical Analysis and Scientific Computing; Other Computer Sciences

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

APA (6th Edition):

Strauss, B. (2019). PREDICTING SWITCH-LIKE BEHAVIOR IN PROTEINS USING LOGISTIC REGRESSION ON SEQUENCE-BASED DESCRIPTORS. (Masters Thesis). San Jose State University. Retrieved from https://doi.org/10.31979/etd.g9yf-st4y ; https://scholarworks.sjsu.edu/etd_projects/829

Chicago Manual of Style (16th Edition):

Strauss, Benjamin. “PREDICTING SWITCH-LIKE BEHAVIOR IN PROTEINS USING LOGISTIC REGRESSION ON SEQUENCE-BASED DESCRIPTORS.” 2019. Masters Thesis, San Jose State University. Accessed November 14, 2019. https://doi.org/10.31979/etd.g9yf-st4y ; https://scholarworks.sjsu.edu/etd_projects/829.

MLA Handbook (7th Edition):

Strauss, Benjamin. “PREDICTING SWITCH-LIKE BEHAVIOR IN PROTEINS USING LOGISTIC REGRESSION ON SEQUENCE-BASED DESCRIPTORS.” 2019. Web. 14 Nov 2019.

Vancouver:

Strauss B. PREDICTING SWITCH-LIKE BEHAVIOR IN PROTEINS USING LOGISTIC REGRESSION ON SEQUENCE-BASED DESCRIPTORS. [Internet] [Masters thesis]. San Jose State University; 2019. [cited 2019 Nov 14]. Available from: https://doi.org/10.31979/etd.g9yf-st4y ; https://scholarworks.sjsu.edu/etd_projects/829.

Council of Science Editors:

Strauss B. PREDICTING SWITCH-LIKE BEHAVIOR IN PROTEINS USING LOGISTIC REGRESSION ON SEQUENCE-BASED DESCRIPTORS. [Masters Thesis]. San Jose State University; 2019. Available from: https://doi.org/10.31979/etd.g9yf-st4y ; https://scholarworks.sjsu.edu/etd_projects/829

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