SwissDock is a web service that predicts the molecular interactions likely to occur between a target protein and a small molecule. On SwissDock 2, two docking methods can be used: When using AC, the rough energy landscape of the macromolecule is replaced by a smooth attracting energy landscape generated by virtual attracting points surrounding the macromolecular surface. Then the sampling algorithm for docking is constituted of simple rotations, translations and geometry optimizations of the ligand in the smooth landscape. Optimizations in the "mold" are followed by optimizations in the actual protein energy landscape and an implicit solvation treatment. The scoring function of AC is composed of the CHARMM force field terms and the fast analytical continuum treatment of solvation (FACTS) model.

The Vina scoring function comprises a potential like van der Waals forces, an undirected hydrogen-bond component, a hydrophobic factor, and a penalty for conformational entropy. Vina computes interactions between molecules through trilinear interpolations of precalculated grid maps on the target structure, and it uses the target structure for postprocessing minimization of the docked poses.


See terms of use.