Quality Control of 3-Methyl-1H-pyrrole. The mechanism of aromatic electrophilic substitution of aromatic heterocycles is consistent with that of benzene. Compound: 3-Methyl-1H-pyrrole, is researched, Molecular C5H7N, CAS is 616-43-3, about Decoys for Docking. Author is Graves, Alan P.; Brenk, Ruth; Shoichet, Brian K..
Mol. docking is widely used to predict novel lead compounds for drug discovery. Success depends on the quality of the docking scoring function, among other factors. An imperfect scoring function can mislead by predicting incorrect ligand geometries or by selecting nonbinding mols. over true ligands. These false-pos. hits may be considered “”decoys””. Although these decoys are frustrating, they potentially provide important tests for a docking algorithm; the more subtle the decoy, the more rigorous the test. Indeed, decoy databases have been used to improve protein structure prediction algorithms and protein-protein docking algorithms. Here, we describe 20 geometric decoys in five enzymes and 166 “”hit list”” decoys-i.e., mols. predicted to bind by our docking program that were tested and found not to do so – for β-lactamase and two cavity sites in lysozyme. Especially in the cavity sites, which are very simple, these decoys highlight particular weaknesses in our scoring function. We also consider the performance of five other widely used docking scoring functions against our geometric and hit list decoys. Intriguingly, whereas many of these other scoring functions performed better on the geometric decoys, they typically performed worse on the hit list decoys, often highly ranking mols. that seemed to poorly complement the model sites. Several of these “”hits”” from the other scoring functions were tested exptl. and found, in fact, to be decoys. Collectively, these decoys provide a tool for the development and improvement of mol. docking scoring functions. Such improvements may, in turn, be rapidly tested exptl. against these and related exptl. systems, which are well-behaved in assays and for structure determination
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