Finds docking transformations that yield good molecular shape complementarity. A wide interface is ensured to include several matched local features of the docked molecules. PatchDock divides the Connolly dot surface representation of the molecules into concave, convex and flat patches. Then, complementary patches are matched to generate candidate transformations. Each candidate is further evaluated by a scoring function that considers both geometric fit and atomic desolvation. An root mean square deviation clustering is applied to the candidate solutions to discard redundant solutions. PatchDock performs structure prediction of protein–protein and protein–small molecule complexes.
Predicts protein–protein interactions (PPIs). Cluspro is an automated web server for protein-protein docking. The software can discriminate putative structures generated by the user, executing any one of the server-compatible docking algorithms. Additional functions allows users to perform a structure modification, specify attraction and repulsion or define pairwise distance restraints.
An information-driven flexible docking approach for the modeling of biomolecular complexes. HADDOCK distinguishes itself from ab-initio docking methods in the fact that it encodes information from identified or predicted protein interfaces in ambiguous interaction restraints (AIRs) to drive the docking process. HADDOCK can deal with a large class of modeling problems including protein-protein, protein-nucleic acids and protein-ligand complexes.
Assists in finding a minimum free-energy complex structure. RosettaDock is a multi-start, multi-scale Monte Carlo based algorithm which searches the rigid-body and side-chain conformational space of two interacting proteins. It can be combined with other docking servers, using its capability of local searches to refine proposed docking positions. It also includes a simple interface and computing resources.