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The number of compounds docked is the number of compounds that pass the default docking filters (<100 atoms, <15 rotatable bonds, and no invalid atom types for the OPLS2001 force-field) and are thus smaller than the initial dataset size. For example, of the 150 reference compounds, eight were not docked due to the presence of too many rotatable bonds, giving a final set of 142 compounds which were evaluated by molecular docking.
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35
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68149168592
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note
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To identify ligand structures that are known protein kinase binders within the PDB, a set of five protein kinase crystal structures were identified as true protein kinase domains representing key sequences in the protein kinase family and used as reference sequences. The structures were 1ATP, 1NVR, 1OKY, 1QPD and 2BUJ. The co-crystal complexes with sequence identities of at least 20% over a span of at least 200 amino acids to the reference sequences were assumed to be true protein kinase structures, and their ligands true kinase binding molecules. Ligands co-crystallized with these kinase structures were extracted, and structures were eliminated if they contained undesirable elements, were trivial co-solvent molecules, ions or ATP-like compounds (consisting of an adenine or guanidine linked to a sugar moiety). This procedure ensured that our dataset consisted of ligands binding in the active site of protein or receptor kinases.
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68149179216
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note
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A quinazoline modification of this scaffold was present in our reference set.
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