J4 ›› 2013, Vol. 26 ›› Issue (2): 1-6.doi: 10.3976/j.issn.1002-4026.2013.02.001
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WANG Jia-Lei, MENG Xian-Mei, ZHANG Qiang-Gang, ZHANG Yi-Ci, ZHANG Shao-Long
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Abstract:
We performed 100 nanosecond molecular dynamics simulation for the allosteric inhibitor system and active site inhibitor system of HIV-1 protease on NVIDIA CUDA GPU with new developed force field ff12SB. We also calculated the bind free energy of inhibitor TL-3 and HIV-1 protease with MM-PB/GBSA. Exo site binded fragment 2-methylcyclohexanol is favorable for the binding of inhibitor near the site. The bind free energy of inhibitor TL-3 and protease is -85.78 kcal/mol in allosteric inhibitor system and -79.45 kcal/mol in active site inhibitor system. These results are benefit for the deep learning of the dynamics process of HIV-1 PR, which provides important guidelines for the design of new strong inhibitors.
Key words: HIV-1 protease, allosteric inhibitor, MM-PB/GBSA, CUDA, Amber, ff12SB force field
CLC Number:
O641.12
WANG Jia-Lei, MENG Xian-Mei, ZHANG Qiang-Gang, ZHANG Yi-Ci, ZHANG Shao-Long. Long-time molecular dynamics simulation of allosteric inhibitor system of HIV-1 protease[J].J4, 2013, 26(2): 1-6.
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