title: The ClusPro web server for protein-protein docking.
abstract: The ClusPro server (https://cluspro.org) is a widely used tool for protein-protein docking. The server provides a simple home page for basic use, requiring only two files in Protein Data Bank (PDB) format. However, ClusPro also offers a number of advanced options to modify the search; these include the removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering (SAXS) data, and location of heparin-binding sites. Six different energy functions can be used, depending on the type of protein. Docking with each energy parameter set results in ten models defined by centers of highly populated clusters of low-energy docked structures. This protocol describes the use of the various options, the construction of auxiliary restraints files, the selection of the energy parameters, and the analysis of the results. Although the server is heavily used, runs are generally completed in <4 h.
authors.affiliation: Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.|Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.|Laufer Center for Physical and Quantitative Biology, Stony Brook University, New York, USA.
authors.forename: Dima
authors.initials: D
authors.lastname: Kozakov
authors.affiliation: Acpharis Inc., Holliston, Massachusetts, USA.
authors.forename: David R
authors.initials: DR
authors.lastname: Hall
authors.affiliation: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.
authors.forename: Bing
authors.initials: B
authors.lastname: Xia
authors.affiliation: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.
authors.forename: Kathryn A
authors.initials: KA
authors.lastname: Porter
authors.affiliation: Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.
authors.forename: Dzmitry
authors.initials: D
authors.lastname: Padhorny
authors.affiliation: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.
authors.forename: Christine
authors.initials: C
authors.lastname: Yueh
authors.affiliation: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.
authors.forename: Dmitri
authors.initials: D
authors.lastname: Beglov
authors.affiliation: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.
authors.forename: Sandor
authors.initials: S
authors.lastname: Vajda
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D006493:Heparin / Q000378:metabolism; D020407:Internet; D025941:Protein Interaction Mapping / Q000379:methods*; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D013816:Thermodynamics
chemical_list: D006493:Heparin