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


RESULTS
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.


CONCLUSIONS
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.
Jenwitheesuk
Ekachai
E
Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA. ekachai@compbio.washington.edu
Samudrala
Ram
R
D003198:Computer Simulation; D016333:HIV Protease / Q000737:chemistry* / Q000378:metabolism*; D017320:HIV Protease Inhibitors / Q000737:chemistry* / Q000378:metabolism*; D015497:HIV-1 / Q000201:enzymology*; D008024:Ligands; D008958:Models, Molecular; D009038:Motion; D011485:Protein Binding
D017320:HIV Protease Inhibitors; D008024:Ligands; D016333:HIV Protease