A geometry-based generic predictor for catalytic and allosteric sites.

Simon Mitternacht, Igor N Berezovsky

Computational Biology Unit, Bergen Center for Computational Science, Bergen, Norway.

Protein engineering, design & selection : PEDS 2011 Apr

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An important aspect of understanding protein allostery, and of artificial effector design, is the characterization and prediction of substrate- and effector-binding sites. To find binding sites in allosteric enzymes, many of which are oligomeric with allosteric sites at domain interfaces, we devise a local centrality measure for residue interaction graphs, which behaves well for both small/monomeric and large/multimeric proteins. The measure is purely structure based and has a clear geometrical interpretation and no free parameters. It is not biased towards typically catalytic residues, a property that is crucial when looking for non-catalytic effector sites, which are potent drug targets.

Citation

Simon Mitternacht, Igor N Berezovsky. A geometry-based generic predictor for catalytic and allosteric sites. Protein engineering, design & selection : PEDS. 2011 Apr;24(4):405-9