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Open Access Highly Accessed Research article

Improved prediction of HIV-1 protease-inhibitor binding energies by molecular dynamics simulations

Ekachai Jenwitheesuk12 and Ram Samudrala1*

Author Affiliations

1 Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA

2 Department of Clinical Microbiology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand

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BMC Structural Biology 2003, 3:2  doi:10.1186/1472-6807-3-2

Published: 1 April 2003



The accurate prediction of enzyme-substrate interaction energies is one of the major challenges in computational biology. This study describes the improvement of protein-ligand binding energy prediction by incorporating protein flexibility through the use of molecular dynamics (MD) simulations.


Docking experiments were undertaken using the program AutoDock for twenty-five HIV-1 protease-inhibitor complexes determined by x-ray crystallography. Protein-rigid docking without any dynamics produced a low correlation of 0.38 between the experimental and calculated binding energies. Correlations improved significantly for all time scales of MD simulations of the receptor-ligand complex. The highest correlation coefficient of 0.87 between the experimental and calculated energies was obtained after 0.1 picoseconds of dynamics simulation.


Our results indicate that relaxation of protein complexes by MD simulation is useful and necessary to obtain binding energies that are representative of the experimentally determined values.