Guided docking: first step to locate potential binding sites.
The long-range electrostatic forces of the targets in round 2 of the Critical Assessment of PRediction of Interactions (CAPRI) experiment were examined and a simple guided docking method, based on these forces, was applied. The method described consists of calculating an initial rigid body trajectory and an optional final, fully flexible refinement stage. Although only limited success was found in predicting the final complexes, some interesting information was discovered. In particular, the long-range forces seem to give some insight into the unusual binding mode of target 4 while raising some questions about target 7, which warrant further investigation.
Fitzjohn
Paul W
PW
Biomolecular Modelling Laboratory, Cancer Research U.K. London Research Institute, London, United Kingdom.
Bates
Paul A
PA
D000465:Algorithms; D000818:Animals; D001665:Binding Sites; D005098:Exotoxins / Q000737:chemistry / Q000378:metabolism; D007135:Immunoglobulin Variable Region / Q000737:chemistry / Q000276:immunology; D046911:Macromolecular Substances; D008958:Models, Molecular; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D011948:Receptors, Antigen, T-Cell / Q000737:chemistry / Q000378:metabolism; D055672:Static Electricity; D000516:alpha-Amylases / Q000737:chemistry / Q000276:immunology
D005098:Exotoxins; D007135:Immunoglobulin Variable Region; D046911:Macromolecular Substances; D011506:Proteins; D011948:Receptors, Antigen, T-Cell; D000516:alpha-Amylases