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Prediction of ligand binding sites using homologous structures and conservation at CASP8
Author(s) -
Wass Mark N.,
Sternberg Michael J. E.
Publication year - 2009
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.22513
Subject(s) - protein superfamily , computational biology , protein function , binding site , homologous chromosome , function (biology) , conserved sequence , protein structure prediction , computer science , protein structure , chemistry , biology , biological system , data mining , genetics , biochemistry , peptide sequence , gene
The critical assessment of protein structure prediction experiment is a blind assessment of the prediction of protein structure and related topics including function prediction. We present our results in the function/binding site prediction category. Our approach to identify binding sites combined the use of the predicted structure of the targets with both residue conservation and the location of ligands bound to homologous structures. We obtained an average coverage of 83% and 56% accuracy. Analysis of our predictions suggests that overprediction reduces the accuracy obtained due to large areas of conservation around the binding site that do not bind the ligand. In some proteins such conserved residues may have a functional role. A server version of our method will soon be available. Proteins 2009. © 2009 Wiley‐Liss, Inc.