Exploiting sequence and structure homologs to identify protein–protein binding sites

Proteins: Structure, Function and Bioinformatics - Tập 62 Số 3 - Trang 630-640 - 2006
Jo‐Lan Chung1,2, Wei Wang1, Philip E. Bourne3,2
1Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
2San Diego Supercomputer Center, University of California, San Diego, La Jolla, California
3Department of Pharmacology, University of California, San Diego, La Jolla, California

Tóm tắt

AbstractA rapid increase in the number of experimentally derived three‐dimensional structures provides an opportunity to better understand and subsequently predict protein–protein interactions. In this study, structurally conserved residues were derived from multiple structure alignments of the individual components of known complexes and the assigned conservation score was weighted based on the crystallographic B factor to account for the structural flexibility that will result in a poor alignment. Sequence profile and accessible surface area information was then combined with the conservation score to predict protein–protein binding sites using a Support Vector Machine (SVM). The incorporation of the conservation score significantly improved the performance of the SVM. About 52% of the binding sites were precisely predicted (greater than 70% of the residues in the site were identified); 77% of the binding sites were correctly predicted (greater than 50% of the residues in the site were identified), and 21% of the binding sites were partially covered by the predicted residues (some residues were identified). The results support the hypothesis that in many cases protein interfaces require some residues to provide rigidity to minimize the entropic cost upon complex formation. Proteins 2006. © 2005 Wiley‐Liss, Inc.

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Proteins: Structure, Function and Bioinformatics

Tập 62 Số 3

630-640

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