Propensity vectors of low-ASA residue pairs in the distinction of protein interactions

Publication Type:
Journal Article
Proteins: Structure, Function and Bioinformatics, 2010, 78 (3), pp. 589 - 602
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We introduce low-ASA residue pairs as classification features for distinguishing the different types of protein interactions. A low-ASA residue pair is defined as two contact residues each from one chain that have a small solvent accessible surface area (ASA). This notion of residue pairs is novel as it first combines residue pairs with the O-ring theory, an influential proposition stating that the binding hot spots at the interface are often surrounded by a ring of energetically less important residues. As binding hot spots lie in the core of the stability for protein interactions, we believe that low-ASA residue pairs can sharpen the distinction of protein interactions. The main part of our feature vector is 210-dimensional, consisting of all possible low-ASA residue pairs; the value of every feature is determined by a propensity measure. Our classification method is called OringPV, which uses propensity vectors of protein interactions for support vector machine. OringPV is tested on three benchmark datasets for a variety of classification tasks such as the distinction between crystal packing and biological interactions, the distinction between two different types of biological interactions, etc. The evaluation frameworks include within-dataset, crossdataset comparison, and leave-one-out crossvalidation. The results show that low-ASA residue pairs and the propensity vector description of protein interactions are truly strong in the distinction. In particular, many cross-dataset generalization capability tests have achieved excellent recalls and overall accuracies, much outperforming existing benchmark methods. © 2009 Wiley-Liss, Inc.
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