ClusPro-DC: Dimer Classification by the Cluspro Server for Protein–Protein Docking. Issue 3 (3rd February 2017)

• Record Type: Journal Article
• Authors: Yueh, Christine; Hall, David R.; Xia, Bing; Padhorny, Dzmitry; Kozakov, Dima; Vajda, Sandor
• Is Part Of: Journal of molecular biology. Volume 429:Issue 3(2017)
• Page Start: 372
• Page End: 381
• Publication Date: 2017-02-03
• Subjects: PQS Protein Quaternary Structure -- PDB Protein Data Bank -- EPPIC Evolutionary Protein–Protein Interface Classifier -- CAPRI Critical Assessment of Predicted Interactions -- IRMSD interface RMSD -- PISA Proteins, Interfaces, Structures and Assemblies; crystallographic dimer -- biological dimer -- solution structure -- energy landscape -- interface discrimination; Molecular biology -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Bacteriology -- Periodicals; Molecular Biology -- Periodicals; Biochemistry -- Periodicals; Biologie moléculaire -- Périodiques; Biologie -- Périodiques; Biochimie -- Périodiques; Moleculaire biologie; Biochemistry; Biology; Molecular biology; Periodicals; 572.805
• DOI: 10.1016/j.jmb.2016.10.019
• Languages: English
• ISSNs: 0022-2836

Abstract

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. Graphical Abstract: Highlights: 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.