Computer simulation of liquids
Computer simulation of liquids
Concurrency and Computation: Practice & Experience
A workflow management and grid computing approach to molecular simulation-based bio/nano experiments
ICCS'03 Proceedings of the 2003 international conference on Computational science
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A validity of Grid computing with Monte Carlo (MC) docking simulations was examined in order to execute prediction and data handling for the computational chiral discrimination. Docking simulations were performed with various computational parameters for the chiral discrimination of a series of 17 enantiomers by β-cyclodextrin (β-CD) or by 6-amino-6-deoxy-β-cyclodextrin (am-β-CD). Rigid-body MC docking simulations gave more accurate predictions than flexible docking simulations. The accuracy was also affected by both the simulation temperature and the kind of force field. The prediction rate of chiral preference was improved by as much as 76.7% when rigid-body MC docking simulations were performed at low temperatures (100 K) with a sugar22 parameter set in the CHARMM force field. Our approach for Grid-based MC docking simulations suggested the conformational rigidity of both the host and guest molecule.