Journal
JOURNAL OF MEDICINAL CHEMISTRY
Volume 50, Issue 21, Pages 5128-5134Publisher
AMER CHEMICAL SOC
DOI: 10.1021/jm070484a
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Funding
- NIGMS NIH HHS [GM075636, R42 GM075636-03, R42 GM075636] Funding Source: Medline
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We have generated docking poses for the FKBP-GPI complex using eight. docking programs, and compared their scoring functions with scoring based on NMR chemical shift perturbations (NMRScore). Because the chemical shift perturbation (CSP) is exquisitely sensitive on the orientation of the ligand inside the binding pocket, NMRScore offers an accurate and straightforward approach to score different poses. All scoring functions were inspected by their abilities to highly rank the native-like structures and separate them from decoy poses generated for a protein-ligand complex. The overall performance of NMRScore is much better than that of energy-based scoring functions associated with docking programs in both aspects. In summary, we find that the combination of docking programs with NMRScore results in an approach that can robustly determine the binding site structure for a protein-ligand complex, thereby providing a new tool facilitating the structure-based drug discovery process.
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