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SemiHS: An Iterative Semi-Supervised Approach for Predicting Proteinprotein Interaction Hot Spots

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Protein-protein interaction hot spots, as revealed by alanine scanning mutagenesis, make dominant contributions to the free energy of binding. Since mutagenesis experiments are expensive and time-consuming, the development of computational methods to identify hot spots is becoming increasingly important. In this study, by using a new combination of sequence, structure and energy features, we propose an iterative semi-supervised algorithm, SemiHS, to incorporate unlabeled data to improve the accuracy of hot spots prediction when sufficient training data is un-available and to overcome the imbalanced data problem. We evaluate the predictive power of SemiHS on a labeled set of 265 alaninemutated interface residues in 17 complexes and a large unlabeled set of 2465 interface residues with 10-fold cross validation, and get an AUC score of 0.85, with a sensitivity of 0.70 and a specificity of 0.87, which are better than those of the existing methods. Moreover, we validate the proposed method by an independent test and obtain encouraging results.

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Keywords: Bayes network; Human Growth Hormone; ML methods; SVM; Semi-Supervised Learning; SemiHS; Systematic mutagenesis; apoptosis; desolvation energy; double water exclusion; hot spots; jackknife test; mutagenesis; protein engineering; protein interfaces; protein-protein interaction; semi-supervised

Document Type: Research Article

Publication date: September 1, 2011

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  • Protein & Peptide Letters publishes short papers in all important aspects of protein and peptide research, including structural studies, recombinant expression, function, synthesis, enzymology, immunology, molecular modeling, drug design etc. Manuscripts must have a significant element of novelty, timeliness and urgency that merit rapid publication. Reports of crystallisation, and preliminary structure determinations of biologically important proteins are acceptable. Purely theoretical papers are also acceptable provided they provide new insight into the principles of protein/peptide structure and function.
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