Computational Methods for Identification of Functional Residues in Protein Structures
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
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.
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