Current Protein & Peptide Science

Ben M. Dunn  
Department of Biochemistry and Molecular Biology University of Florida
College of Medicine, P.O. Box 100245, Gainesville
Florida, FL 32610-0245
USA

Back

Computational Methods for Identification of Functional Residues in Protein Structures

Author(s): Fuxiao Xin and Predrag Radivojac

Affiliation: School of Informatics and Computing, Indiana University, 901 E. 10th Street, Bloomington, IN 47408, USA.

Keywords: Comparative evaluation, functional residue prediction, functional site prediction, protein function prediction, protein structure, structure-based protein function prediction, computational prediction, biochemical, DNA-binding protein, computationally aided protein engineering

Abstract:

The recent accumulation of experimentally determined protein 3D structures combined with our ability to computationally model structure from amino acid sequence has resulted in an increased importance of structure-based methods for protein function prediction. Two types of methods for function prediction have been proposed: those that can accurately predict overall biochemical or biological roles of a protein and those that predict its functional residues. Here, we review approaches used for the computational identification of functional residues in protein structures and summarize their applications to a wide variety of problems in functional proteomics, such as the prediction of catalytic residues, posttranslational modifications, or nucleic acid-binding sites. We examine four different problems in order to perform a comparison between several recently proposed methods and, finally, conclude by identifying limitations and future challenges in this field.

Reprint ePrint Rights & PermissionsPrintExport

Article Details

VOLUME: 12
ISSUE: 6
Page: [456 - 469]
Pages: 14
DOI: 10.2174/138920311796957685