HomPPI: A Class of Sequence Homology Based Protein-Protein Interface Prediction Methods

Background: Although homology-based methods are among the most widely used methods for predicting the structure and function of proteins, the question as to whether interface sequence conservation can be effectively exploited in predicting protein-protein interfaces has been a subject of debate. Results: We studied more than 300,000 pair-wise alignments of protein sequences from structurally characterized protein complexes, including both obligate and transient complexes. We identified sequence similarity criteria required for accurate homology-based inference of interface residues in a query protein sequence. Based on these analyses, we developed HomPPI, a class of sequence homology-based methods for predicting protein-protein interface residues. We present two variants of HomPPI: (i) NPS-HomPPI (Non partner-specific HomPPI), which can be used to predict interface residues of a query protein in the absence of knowledge of the interaction partner; and (ii) PS-HomPPI (Partner-specific ...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Li C. Xue, Drena Dobbs, Vasant Honavar
• Keywords: Biometrics, BMCBI 2011, Query Protein Sequence, Similarity Criteria, Target Protein