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A scoring function for docking ligands to low-resolution protein structures

✍ Scribed by Eckart Bindewald; Jeffrey Skolnick

Publisher
John Wiley and Sons
Year
2005
Tongue
English
Weight
178 KB
Volume
26
Category
Article
ISSN
0192-8651

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✦ Synopsis

Abstract

We present a docking method that uses a scoring function for protein–ligand docking that is designed to maximize the docking success rate for low‐resolution protein structures. We find that the resulting scoring function parameters are very different depending on whether they were optimized for high‐ or low‐resolution protein structures. We show that this docking method can be successfully applied to predict the ligand‐binding site of low‐resolution structures. For a set of 25 protein–ligand complexes, in 76% of the cases, more than 50% of ligand‐contacting residues are correctly predicted (using receptor crystal structures where the binding site is unspecified). Using decoys of the receptor structures having a 4 Å RMSD from the native structure, for the same set of complexes, in 72% of the cases, we obtain at least one correctly predicted ligand‐contacting residue. Furthermore, using an 81‐protein–ligand set described by Jain, in 76 (93.8%) cases, the algorithm correctly predicts more than 50% of the ligand‐contacting residues when native protein structures are used. Using 3 Å RMSD from native decoys, in all but two cases (97.5%), the algorithm predicts at least one ligand‐binding residue correctly. Finally, compared to the previously published Dolores method, for 298 protein–ligand pairs, the number of cases in which at least half of the specific contacts are correctly predicted is more than four times greater. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 374–383, 2005

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