simple and efficient method for predicting protein-protein interaction sites

• Published in: Genetics and molecular research Vol. 7; no. 3; pp. 898 - 909
• Main Authors: Higa, R.H, Tozzi, C.L
• Format: Journal Article
• Language: English
• Published: Brazil 01.01.2008
• Subjects: amino acid composition; Binding Sites; Computational Biology - methods; Protein Binding; Protein Conformation; Protein Interaction Mapping; protein structure; protein-protein interactions; Proteins - chemistry; Sequence Analysis, Protein - methods
• ISSN: 1676-5680; 1676-5680
• DOI: 10.4238/vol7-3X-Meeting07

Computational methods for predicting protein-protein interaction sites based on structural data are characterized by an accuracy between 70 and 80%. Some experimental studies indicate that only a fraction of the residues, forming clusters in the center of the interaction site, are energetically important for binding. In addition, the analysis of amino acid composition has shown that residues located in the center of the interaction site can be better discriminated from the residues in other parts of the protein surface. In the present study, we implement a simple method to predict interaction site residues exploiting this fact and show that it achieves a very competitive performance compared to other methods using the same dataset and criteria for performance evaluation (success rate of 82.1%).