Abstract
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 A 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.
Publication types
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Research Support, Non-U.S. Gov't
MeSH terms
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Amiloride / chemistry
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Amiloride / metabolism
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Aminoimidazole Carboxamide / analogs & derivatives
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Aminoimidazole Carboxamide / chemistry
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Aminoimidazole Carboxamide / metabolism
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Arabinose / analogs & derivatives
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Arabinose / chemistry
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Arabinose / metabolism
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Concanavalin A / chemistry
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Concanavalin A / metabolism
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Enzyme Inhibitors / metabolism
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Fructose-Bisphosphatase / chemistry
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Fructose-Bisphosphatase / metabolism
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Humans
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Ligands*
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Molecular Structure
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Pancreatic Elastase / chemistry
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Pancreatic Elastase / metabolism
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Pentamidine / chemistry
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Pentamidine / metabolism
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Protein Conformation*
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Proteins / chemistry*
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Proteins / metabolism
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Ribonucleosides / chemistry
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Ribonucleosides / metabolism
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Software*
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Trypsin / chemistry
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Trypsin / metabolism
Substances
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Enzyme Inhibitors
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Ligands
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Proteins
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Ribonucleosides
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Concanavalin A
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Aminoimidazole Carboxamide
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acadesine
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Pentamidine
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Amiloride
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Arabinose
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Fructose-Bisphosphatase
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Pancreatic Elastase
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Trypsin