Journal
PROTEINS-STRUCTURE FUNCTION AND GENETICS
Volume 46, Issue 1, Pages 34-40Publisher
WILEY-LISS
DOI: 10.1002/prot.10028
Keywords
protein flexibility; peptidomimetic inhibitors; HIV-1
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Funding
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [P01GM048870] Funding Source: NIH RePORTER
- NIGMS NIH HHS [GM48870] Funding Source: Medline
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Protein motion and heterogeneity of structural waters are approximated in ligand-docking simulations, using an ensemble of protein structures. Four methods of combining multiple target structures within a single grid-based lookup table of interaction energies are tested. The method is evaluated using complexes of 21 peptidomimetic inhibitors with human immunodeficiency virus type 1 (HIV-1) protease. Several of these structures show motion of an arginine residue, which is essential for binding of large inhibitors. A structural water is also present in 20 of the structures, but it must be absent in the remaining one for proper binding. Mean and minimum methods perform poorly, but two weighted average methods permit consistent and accurate ligand docking, using a single grid representation of the target protein structures. Proteins 2002;46:34-40. (C) 2001 Wiley-Liss, Inc.
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