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

J Mol Biol. 2017 Feb 3;429(3):372-381. doi: 10.1016/j.jmb.2016.10.019. Epub 2016 Oct 19.

Abstract

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.

Keywords: biological dimer; crystallographic dimer; energy landscape; interface discrimination; solution structure.

MeSH terms

  • Databases, Protein
  • Escherichia coli / chemistry
  • Molecular Docking Simulation*
  • Protein Conformation
  • Protein Interaction Mapping*
  • Proteins / chemistry*
  • X-Rays

Substances

  • Proteins