RBSURFpred: Modeling protein accessible surface area in real and binary space using regularized and optimized regression.
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Abstract | Accessible surface area (ASA) of a protein residue is an effective feature for protein structure prediction, binding region identification, fold recognition problems etc. Improving the prediction of ASA by the application of effective feature variables is a challenging but explorable task to consider, specially in the field of machine learning. Among the existing predictors of ASA, REGAdp is a highly accurate ASA predictor which is based on regularized exact regression with polynomial kernel of degree 3. In this work, we present a new predictor RBSURFpred, which extends REGAdp on several dimensions by incorporating 58 physicochemical, evolutionary and structural properties into 9-tuple peptides via Chou's general PseAAC, which allowed us to obtain higher accuracies in predicting both real-valued and binary ASA. We have compared RBSURFpred for both real and binary space predictions with state-of-the-art predictors, such as REGAdp and SPIDER2. We also have carried out a rigorous analysis of the performance of RBSURFpred in terms of different amino acids and their properties, and also with biologically relevant case-studies. The performance of RBSURFpred establishes itself as a useful tool for the community. |
Year of Publication | 2018
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Journal | J Theor Biol
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Volume | 441
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Pages | 44-57
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Date Published | 2018 03 14
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ISSN | 1095-8541
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DOI | 10.1016/j.jtbi.2017.12.029
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PubMed ID | 29305182
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