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CASP2 molecular docking predictions with the LIGIN software
Author(s) -
Sobolev Vladimir,
Moallem Theodore M.,
Wade Rebecca C.,
Vriend Gert,
Edelman Marvin
Publication year - 1997
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(1997)1+<210::aid-prot28>3.0.co;2-q
Subject(s) - docking (animal) , dock , searching the conformational space for docking , protein–ligand docking , crystallography , chemistry , macromolecular docking , computer science , protein structure , molecular dynamics , computational chemistry , biochemistry , virtual screening , medicine , nursing
Seven docking predictions were made 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 Å RMSD of the experimentally determined structure. LIGIN has not been optimized to deal with highly flexible ligands that dock at the surface of proteins. Consequently, in three cases the exposed part of the ligand was docked poorly, although the buried parts were docked well, and made similar atomic contacts with the protein as in the experimentally determined structure. Proteins, Suppl. 1:210–214, 1997. © 1998 Wiley‐Liss, Inc.