FireDock: a web server for fast interaction refinement in molecular docking

Structural details of protein-protein interactions are invaluable for understanding and deciphering biological mechanisms. Computational docking methods aim to predict the structure of a protein-protein complex given the structures of its single components. Protein flexibility and the absence of robust scoring functions pose a great challenge in the docking field. Due to these difficulties most of the docking methods involve a two-tier approach: coarse global search for feasible orientations that treats proteins as rigid bodies, followed by an accurate refinement stage that aims to introduce flexibility into the process. The FireDock web server, presented here, is the first web server for flexible refinement…

• UD
  U.S. Department of Health and Human Services
• IS
  Israel Science Foundation

  Award: 281/05
• NI
  National Institutes of Health

  Awards: N01-CO-12400, NO1-CO-12400
• NC
  National Cancer Institute

  Awards: NO1-CO-12400, N01-CO-12400
• NI
  National Institute of Allergy and Infectious Diseases