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JOURNAL ARTICLE
RESEARCH SUPPORT, N.I.H., EXTRAMURAL
RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
ClusPro-DC: Dimer Classification by the Cluspro Server for Protein-Protein Docking.
Journal of Molecular Biology 2017 Februrary 4
ClusPro-DC (https://cluspro.bu.edu/) implements a straightforward approach to the discrimination between crystallographic and biological dimers by docking the two subunits to exhaustively sample the interaction energy landscape. If a substantial number of low energy docked poses cluster in a narrow vicinity of the native structure of the dimer, then one can assume that there is a well-defined free energy well around the native state, which makes the interaction stable. In contrast, if the interaction sites in the docked poses do not form a large enough cluster around the native structure, then it is unlikely that the subunits form a stable biological dimer. The number of near-native structures is used to estimate the probability of a dimer being biological. Currently, the server examines only the stability of a given interface rather than generating all putative quaternary structures as accomplished by PISA or EPPIC, but it complements the information provided by these methods.
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