title: pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring.
abstract: pyDockWEB is a web server for the rigid-body docking prediction of protein-protein complex structures using a new version of the pyDock scoring algorithm. We use here a new custom parallel FTDock implementation, with adjusted grid size for optimal FFT calculations, and a new version of pyDock, which dramatically speeds up calculations while keeping the same predictive accuracy. Given the 3D coordinates of two interacting proteins, pyDockWEB returns the best docking orientations as scored mainly by electrostatics and desolvation energy.
  
  
  METHODS
  The server does not require registration by the user and is freely accessible for academics at http://life.bsc.es/servlet/pydock.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Joint BSC-IRB Research Programme in Computational Biology, Department of Life Sciences, Barcelona Supercomputing Center, National Institute of Bioinformatics, Jordi Girona 29, 08034 Barcelona, Spain.
authors: Brian
authors: B
authors: Jiménez-García
authors: Carles
authors: C
authors: Pons
authors: Juan
authors: J
authors: Fernández-Recio
mesh_terms: D000465:Algorithms; D020407:Internet; D062105:Molecular Docking Simulation / Q000379:methods*; D046912:Multiprotein Complexes / Q000737:chemistry; D025941:Protein Interaction Mapping / Q000379:methods*; D012984:Software; D055672:Static Electricity
chemical_list: D046912:Multiprotein Complexes