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A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor

✍ Scribed by Rie Tatsumi; Yoshifumi Fukunishi; Haruki Nakamura

Publisher
John Wiley and Sons
Year
2004
Tongue
English
Weight
708 KB
Volume
25
Category
Article
ISSN
0192-8651

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✦ Synopsis

Abstract

We have developed a new docking method to consider receptor flexibility, a hybrid method of molecular dynamics and harmonic dynamics. The global motions of the whole receptor were approximately introduced into those of the receptor in the docking simulation as harmonic dynamics. On the other hand, the local flexibility of the side chains was also considered by conventional molecular dynamics. We confirmed that this new method can reproduce the fluctuations of the whole receptor by making a comparison of the directions and amplitudes of the global fluctuations. Then this method was applied to the docking of HIV‐1 protease and its ligand. As a result, we observed a docking process where the ligand enters into the binding pocket well, which implies that this method is effective enough to reproduce a molecular complex formation. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1995–2005, 2004

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