CASP2 molecular docking predictions with the LIGIN software

In the examples suggested by CASP2, we tested our approach for predicting binding pocket location, ligand orientation and the major interactions stabilizing the ligand-receptor complex.
In our approach, surface complementarity between a ligand and receptor is the guiding principle for ligand docking (Sobolev V., Wade R.C., Vriend G. & Edelman M. (1996) Proteins 25, 120-129). Surface complementarity incorporates information about the shape and chemical nature of the atoms of the interacting molecules.
We made seven docking predictions with the LIGIN program:

In six cases the location of the binding pocket was identified correctly by systematically docking everywhere within the protein structure. In two cases the ligand was docked to within 1.8  r.m.s.d. of the experimentally determined structure. In three cases the exposed part of the ligand was docked poorly, although the buried parts were docked well, and made identical atomic contacts with the protein as in the experimentally determined structure.

Please any questions/comments to vladimir.sobolev@weizmann.ac.il