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Grid‐search molecular accessible surface algorithm for solving the protein docking problem
Author(s) -
Wang Huajun
Publication year - 1991
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540120612
Subject(s) - docking (animal) , grid , representation (politics) , computer science , algorithm , protein–ligand docking , simulated annealing , macromolecular docking , searching the conformational space for docking , surface (topology) , chemistry , protein structure , mathematics , molecular dynamics , computational chemistry , geometry , biochemistry , medicine , nursing , virtual screening , politics , political science , law
An algorithm for solving the protein docking problem is presented. Many tentative dockings are first generated by requiring a hole on the surface of one protein to match a knob on the surface of the other. All the tentative dockings are then applied. The initial configurations thus generated are further optimized. The optimization is facilitated by giving a discrete representation to the protein interior and a double‐layer discrete representation to the protein surface. The algorithm presented correctly predicts the association of trypsin with its inhibitor as well as that of the α and β subunits in hemoglobin.