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Propensity vectors of low-ASA residue pairs in the distinction of protein interactions.
- Source :
-
Proteins [Proteins] 2010 Feb 15; Vol. 78 (3), pp. 589-602. - Publication Year :
- 2010
-
Abstract
- 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, cross-dataset comparison, and leave-one-out cross-validation. 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.
Details
- Language :
- English
- ISSN :
- 1097-0134
- Volume :
- 78
- Issue :
- 3
- Database :
- MEDLINE
- Journal :
- Proteins
- Publication Type :
- Academic Journal
- Accession number :
- 19768686
- Full Text :
- https://doi.org/10.1002/prot.22583