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Molecular docking using surface complementarity
Author(s) -
Sobolev Vladimir,
Wade Rebecca C.,
Vriend Gert,
Edelman Marvin
Publication year - 1996
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(199605)25:1<120::aid-prot10>3.0.co;2-m
Subject(s) - complementarity (molecular biology) , docking (animal) , computational biology , computer science , biology , genetics , medicine , nursing
Abstract A method is described to dock a ligand into a binding site in a protein on the basis of the complementarity of the inter‐molecular 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. © 1996 Wiley Liss, Inc.