title: The RosettaDock server for local protein-protein docking.
abstract: The RosettaDock server (http://rosettadock.graylab.jhu.edu) identifies low-energy conformations of a protein-protein interaction near a given starting configuration by optimizing rigid-body orientation and side-chain conformations. The server requires two protein structures as inputs and a starting location for the search. RosettaDock generates 1000 independent structures, and the server returns pictures, coordinate files and detailed scoring information for the 10 top-scoring models. A plot of the total energy of each of the 1000 models created shows the presence or absence of an energetic binding funnel. RosettaDock has been validated on the docking benchmark set and through the Critical Assessment of PRedicted Interactions blind prediction challenge.
authors.affiliation: Department of Chemical and Biomolecular Engineering and Program in Molecular and Computational Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA.
authors.forename: Sergey
authors.initials: S
authors.lastname: Lyskov
authors.forename: Jeffrey J
authors.initials: JJ
authors.lastname: Gray
mesh_terms: D000465:Algorithms; D020407:Internet; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry*; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D015203:Reproducibility of Results; D012984:Software; D014584:User-Computer Interface
chemical_list: D046912:Multiprotein Complexes