title: New additions to the ClusPro server motivated by CAPRI.
abstract: The heavily used protein-protein docking server ClusPro performs three computational steps as follows: (1) rigid body docking, (2) RMSD based clustering of the 1000 lowest energy structures, and (3) the removal of steric clashes by energy minimization. In response to challenges encountered in recent CAPRI targets, we added three new options to ClusPro. These are (1) accounting for small angle X-ray scattering data in docking; (2) considering pairwise interaction data as restraints; and (3) enabling discrimination between biological and crystallographic dimers. In addition, we have developed an extremely fast docking algorithm based on 5D rotational manifold FFT, and an algorithm for docking flexible peptides that include known sequence motifs. We feel that these developments will further improve the utility of ClusPro. However, CAPRI emphasized several shortcomings of the current server, including the problem of selecting the right energy parameters among the five options provided, and the problem of selecting the best models among the 10 generated for each parameter set. In addition, results convinced us that further development is needed for docking homology models. Finally, we discuss the difficulties we have encountered when attempting to develop a refinement algorithm that would be computationally efficient enough for inclusion in a heavily used server. Proteins 2017; 85:435-444. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215.|Department of Chemistry, Boston University, Boston, Massachusetts, 02215.
authors.forename: Sandor
authors.initials: S
authors.lastname: Vajda
authors.affiliation: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215.
authors.forename: Christine
authors.initials: C
authors.lastname: Yueh
authors.affiliation: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215.
authors.forename: Dmitri
authors.initials: D
authors.lastname: Beglov
authors.affiliation: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215.|Program in Bioinformatics, Boston University, Boston, Massachusetts, 02215.
authors.forename: Tanggis
authors.initials: T
authors.lastname: Bohnuud
authors.affiliation: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215.|Program in Bioinformatics, Boston University, Boston, Massachusetts, 02215.
authors.forename: Scott E
authors.initials: SE
authors.lastname: Mottarella
authors.affiliation: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215.
authors.forename: Bing
authors.initials: B
authors.lastname: Xia
authors.affiliation: Acpharis Inc, Holliston, Massachusetts, 01746.
authors.forename: David R
authors.initials: DR
authors.lastname: Hall
authors.affiliation: Department of Applied Mathematics and Statistics, Stony Brook University, New York.|Laufer Center for Physical and Quantitative Biology, Stony Brook University, New York.
authors.forename: Dima
authors.initials: D
authors.lastname: Kozakov
mesh_terms: D000465:Algorithms; D019985:Benchmarking; D001665:Binding Sites; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D020407:Internet; D062105:Molecular Docking Simulation / Q000379:methods*; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D055503:Protein Multimerization; D011506:Proteins / Q000737:chemistry*; D012107:Research Design; D012984:Software; D040681:Structural Homology, Protein; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D011506:Proteins; D014867:Water
keywords: dimer classification; docking with distance restraints; peptide-protein docking; protein-protein docking; scoring function; small angle X-ray scattering data; structure refinement