A Soft Docking Algorithm for Predicting the Structures of Protein-protein Complexes

( Center for Biomedical
Engineering, Beijing Polytechnic University, Beijing 100022, China )

Abstract
An efficient soft docking algorithm is described to predict the
mode of binding between two proteins based on the three-dimensional structures
of molecules. The molecular model used in this work was grounded on the “simplified
protein” model used in Janin’s docking algorithm. The side chain flexibility
of the amino acid residues Arg, Lys, Asp, Glu and Met at the protein surface
was considered through softening the molecular surface. A double filtering
technique was used to eliminate most of the unlike binding modes. The energy
minimization was performed on the retained structures, and then these structures
were evaluated with the scoring function which included electrostatic, desolvation
and van der Waals energy terms. The 26 complexes were used to test this docking
algorithm and good results were obtained. The native-like conformations of
all the complexes were all found, of which 20 were ranked in the top 10.