Combining specificity determining and conserved residues improves functional site prediction |
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Authors: | Olga V Kalinina Mikhail S Gelfand Robert B Russell |
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Affiliation: | (1) EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany;(2) Institute for Information Transmission Problems RAS, Bolshoi Karenty pereulok 19, Moscow, 127994, Russia |
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Abstract: | Background Predicting the location of functionally important sites from protein sequence and/or structure is a long-standing problem in computational biology. Most current approaches make use of sequence conservation, assuming that amino acid residues conserved within a protein family are most likely to be functionally important. Most often these approaches do not consider many residues that act to define specific sub-functions within a family, or they make no distinction between residues important for function and those more relevant for maintaining structure (e.g. in the hydrophobic core). Many protein families bind and/or act on a variety of ligands, meaning that conserved residues often only bind a common ligand sub-structure or perform general catalytic activities. |
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