ClusPro-DC: Dimer Classification by the Cluspro Server for Protein–Protein Docking

•The X-ray structure of a protein does not determine its oligomeric state in solution.•The oligomeric state can be determined by exhaustively sampling the free energy landscape.•The method provides information complementary to PISA and EPPIC, improving accuracy.•Dimer classification is a new option in the ClusPro protein–protein docking server.

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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