Publication Date
Spring 2013
Degree Type
Thesis
Degree Name
Master of Science (MS)
Department
Chemistry
Advisor
Brooke Lustig
Keywords
Query-Based qualitative predictors, Sequence Homology, Solvent Accessibility Prediction
Subject Areas
Chemistry
Abstract
Characterization of relative solvent accessibility (RSA) plays a major role in classifying a given protein residue as being on the surface or buried. This information is useful for studying protein structure and protein-protein interactions, and it is usually the first approach applied in the prediction of 3-dimensional (3D) protein structures.
Various complicated and time-consuming methods, such as machine learning, have been applied in solvent-accessibility predictions. In this thesis, we presented a simple application of linear regression methods using various sequence homology values for each residue as well as query residue qualitative predictors corresponding to each of the 20 amino acids. Initially, a fit was generated by applying linear regression to training sets with a variety of sequence homology parameters, including various sequence entropies and residue qualitative predictors. Then the coefficients generated via the training sets were applied to the test set, and, subsequently, the predicted RSA values were extracted for the test set. The qualitative predictors describe the actual query residue type (e.g., Gly) as opposed to the measures of sequence homology for the aligned subject residues. The prediction accuracies were calculated by comparing the predicted RSA values with NACCESS RSA (derived from X-ray crystallography). The utilization of qualitative predictors yielded significant prediction accuracy.
Recommended Citation
Nepal, Reecha, "Application of Query-Based Qualitative Descriptors in Conjunction with Protein Sequence Homology for Prediction of Residue Solvent Accessibility" (2013). Master's Theses. 4299.
DOI: https://doi.org/10.31979/etd.em6c-qn2b
https://scholarworks.sjsu.edu/etd_theses/4299
