Functional site prediction selects correct protein models

• Published in: BMC bioinformatics Vol. 9; no. S1; p. S13
• Main Authors: Chelliah, Vijayalakshmi, Taylor, William R
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 13.02.2008; BioMed Central; BMC
• Subjects: Algorithms; Amino Acid Sequence; Binding Sites; Computer Simulation; Models, Chemical; Models, Molecular; Molecular Sequence Data; Proceedings; Protein Binding; Proteins - chemistry; Proteins - ultrastructure; Sequence Analysis, Protein - methods; Structure-Activity Relationship
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/1471-2105-9-S1-S13

The prediction of protein structure can be facilitated by the use of constraints based on a knowledge of functional sites. Without this information it is still possible to predict which residues are likely to be part of a functional site and this information can be used to select model structures from a variety of alternatives that would correspond to a functional protein. Using a large collection of protein-like decoy models, a score was devised that selected those with predicted functional site residues that formed a cluster. When tested on a variety of small alpha/beta/alpha type proteins, including enzymes and non-enzymes, those that corresponded to the native fold were ranked highly. This performance held also for a selection of larger alpha/beta/alpha proteins that played no part in the development of the method. The use of predicted site positions provides a useful filter to discriminate native-like protein models from non-native models. The method can be applied to any collection of models and should provide a useful aid to all modelling methods from ab initio to homology based approaches.