Sobolev V, Wade R C, Vriend G, Edelman M
Department of Plant Genetics, Weizmann Institute of Science, Rehovot, Israel.
Proteins. 1996 May;25(1):120-9. doi: 10.1002/(SICI)1097-0134(199605)25:1<120::AID-PROT10>3.0.CO;2-M.
A method is described to dock a ligand into a binding site in a protein on the basis of the complementarity of the intermolecular atomic contacts. Docking is performed by maximization of a complementarity function that is dependent on atomic contact surface area and the chemical properties of the contacting atoms. The generality and simplicity of the complementarity function ensure that a wide range of chemical structures can be handled. The ligand and the protein are treated as rigid bodies, but displacement of a small number of residues lining the ligand binding site can be taken into account. The method can assist in the design of improved ligands by indicating what changes in complementarity may occur as a result of the substitution of an atom in the ligand. The capabilities of the method are demonstrated by application to 14 protein-ligand complexes of known crystal structure.
描述了一种基于分子间原子接触互补性将配体对接至蛋白质结合位点的方法。对接通过最大化一个互补函数来进行，该函数取决于原子接触表面积和接触原子的化学性质。互补函数的通用性和简单性确保了可以处理广泛的化学结构。配体和蛋白质被视为刚体，但可以考虑配体结合位点处少量残基的位移。该方法可以通过指出配体中原子取代可能导致的互补性变化来辅助设计改进的配体。通过应用于14个已知晶体结构的蛋白质-配体复合物来证明该方法的能力。
