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J Am Chem Soc. 2005 Mar 2;127(8):2600-7.

Flexible docking in solution using metadynamics.

Author information

1
Computational Science, Department of Chemistry and Applied Biosciences, ETH Z├╝rich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland. fgervasi@phys.chem.ethz.ch

Abstract

We apply our recently developed metadynamics method to the docking of ligands on flexible receptors in water solution. This method mimics the real dynamics of a ligand exiting or entering an enzyme and in so doing reconstructs the free energy surface. We apply it to four docking cases: beta-trypsin/benzamidine, beta-trypsin/chlorobenzamidine, immunoglobulin McPC-603/phosphocholine, and cyclin-dependent kinase 2/staurosporine. In every case studied, the method is able to predict the docked geometry and the free energy of docking. Its added value with respect to many other available methods is that it reconstructs the complete free energy surface, including all the relevant minima and the barriers between them.

PMID:
15725015
DOI:
10.1021/ja0445950
[Indexed for MEDLINE]

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