title: FRODOCK 2.0: fast protein-protein docking server.
abstract: The prediction of protein-protein complexes from the structures of unbound components is a challenging and powerful strategy to decipher the mechanism of many essential biological processes. We present a user-friendly protein-protein docking server based on an improved version of FRODOCK that includes a complementary knowledge-based potential. The web interface provides a very effective tool to explore and select protein-protein models and interactively screen them against experimental distance constraints. The competitive success rates and efficiency achieved allow the retrieval of reliable potential protein-protein binding conformations that can be further refined with more computationally demanding strategies.
  
  
  
  The server is free and open to all users with no login requirement at http://frodock.chaconlab.org
  
  
  
  pablo@chaconlab.org
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biological Chemical Physics, Rocasolano Physical Chemistry Institute C.S.I.C, Madrid 28006, Spain Centro de Investigaciones Biológicas, CSIC, Madrid E-28040, Spain.
authors.forename: Erney
authors.initials: E
authors.lastname: Ramírez-Aportela
authors.affiliation: Department of Biological Chemical Physics, Rocasolano Physical Chemistry Institute C.S.I.C, Madrid 28006, Spain.
authors.forename: José Ramón
authors.initials: JR
authors.lastname: López-Blanco
authors.affiliation: Department of Biological Chemical Physics, Rocasolano Physical Chemistry Institute C.S.I.C, Madrid 28006, Spain.
authors.forename: Pablo
authors.initials: P
authors.lastname: Chacón
mesh_terms: D003201:Computers; D011487:Protein Conformation; D011506:Proteins; D012984:Software
chemical_list: D011506:Proteins