title: ClusPro-DC: Dimer Classification by the Cluspro Server for Protein-Protein Docking.
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.
authors: Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
authors: Christine
authors: C
authors: Yueh
authors: Acpharis Inc., Holliston, MA 01746, USA.
authors: David R
authors: DR
authors: Hall
authors: Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
authors: Bing
authors: B
authors: Xia
authors: Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA.
authors: Dzmitry
authors: D
authors: Padhorny
authors: Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA. Electronic address: midas@laufercenter.org.
authors: Dima
authors: D
authors: Kozakov
authors: Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA. Electronic address: vajda@bu.edu.
authors: Sandor
authors: S
authors: Vajda
mesh_terms: D030562:Databases, Protein; D004926:Escherichia coli / Q000737:chemistry; D062105:Molecular Docking Simulation; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry*; D014965:X-Rays
chemical_list: D011506:Proteins
keywords: biological dimer; crystallographic dimer; energy landscape; interface discrimination; solution structure