Abstract
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.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Cabusas, M.E.: Chiral Separations on HPLC Derivatized Polysaccharide CSPs: Ph. D. Thesis, Virginia Polytechnic Institute and State University, USA, 1-9 (1998)
Lee, S., Yi, D.H., Jung, S.: NMR Spectroscopic Analysis on the Chiral Recognition of Noradrenaline by ěâ-Cyclodextrin and Carboxymethyl- ěâ-cyclodextrin. Bull. Korean Chem. Soc. 25, 216–220 (2004)
Choi, Y.H., Yang, C.H., Kim, H.W., Jung, S.: Monte Carlo simulations of the chiral recognition of fenoprofen enantiomers by cyclomaltoheptaose. Carbohydr. Res. 328, 393–397 (2000)
Bouzida, D., Rejto, P.A., Verkhivker, G.M.: Monte Carlo Simulations of Ligand-Protein Binding Energy Landscapes with the Weighted Histogram Analysis Method. Int. J. Quant. Chem. 73, 113–121 (1999)
Rekharsky, M.V., Inoue, Y.J.: Complexation and Chiral Recognition Thermodynamics of 6-Amino-6-Deoxy-Beta-Cyclodextrin with Aanionic, Cationic, and Neutral Chiral Guests: Counterbalance between van der Waals and Coulombic Interactions. J. Am. Chem. Soc. 124, 813–826 (2002)
Lipkowitz, K.B., Coner, R., Peterson, M.A.: Locating Regions of Maximum Chiral Discrimination: A Computational Study of Enantioselection on a Popular Chiral Stationary Phase Used in Chromatography. J. Am. Chem. Soc. 119, 11269–11276 (1997)
Dodziuk, H., Lukin, O.: The Dependence of the Average Energy Difference for the Diastereomeric Complexes of α-Pinene Enantiomers with α-Cyclodextrin on the Length of Dynamic Simulations. Chem. Phys. Lett. 327, 18–22 (2000)
Wolbach, J.P., Lloyd, D.K., Wainer, I.W.: Approaches to Quantitative Structure Enantio-selectivity Relationships Modeling of Chiral Separations Using Capillary Electrophoresis. J. Chromatogr. A. 914, 299–314 (2001)
Booth, T.D., Azzaoui, K., Wainer, I.W.: Prediction of Chiral Chromatography Separations by Combined Multivariate Regression Neural Networks. Anal. Chem. 69, 3879–3883 (1997)
Natrajan, A., Crowley, M., Wilkins-Diehr, N., Humphrey, M.A., Fox, A.D., Grimshaw, A.S., Brooks III, C.L.: Studying Protein Folding on the Grid: Experiences Using CHARMM on NPACI Resources under Legion. Concurr. Computat. Pract. Exper. 16, 385–397 (2004)
Jeong, K., Kim, D., Kim, M., Hwang, S., Jung, S., Lim, Y., Lee, S.: A Workflow Management and Grid Computing Approach to Molecular Simulation-Based Bio/Nano Experiments. In: Sloot, P.M.A., Abramson, D., Bogdanov, A.V., Gorbachev, Y.E., Dongarra, J., Zomaya, A.Y. (eds.) ICCS 2003. LNCS, vol. 2660, pp. 1117–1126. Springer, Heidelberg (2003)
Metropolis, N., Rosenbluth, A.W., Rosenbluth, M.N., Teller, A.H., Teller, E.: Equation of State Calculation by Fast Computing Machines. J. Chem. Phys. 21, 1087–1092 (1953); Solvation Correction. Comput. Chem. 18, 723–743 (1997)
Srinivasan, J., Cheatham, T.E., Cieplak, P., Kollman, P.A., Case, D.A.: Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA Helices. J. Am. Chem. Soc. 120, 9401–9409 (1998)
Sitkoff, D., Sharp, K.A., Honig, B.: Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. J. Phys. Chem. 98, 1978–1988 (1994); Growth Hormone-Receptor Complex. J. Comput. Chem. 23, 15–27 (2002)
Choi, Y., Jung, S.: Molecular Dynamics Simulations for the Prediction of Chiral Discrimination of N-acetylphenylalanine Enantiomers by Cyclomaltoheptaose Based on the MM-PBSA Approach. Carbohydr. Res. 339, 1961–1966 (2004)
Bea, I., Jaime, C., Kollman, P.A.: Molecular Recognition by β-Cyclodextrin Derivatives: FEP vs MM/PBSA Goals and Problems. Theor. Chem. Acc. 108, 286–292 (2002)
Halperin, I., Ma, B., Wolfson, H., Nussinov, R.: Principles of Docking: An Overview of Search Algorithms and a Guide to Scoring Functions. Proteins 47, 409–443 (2002)
Ahn, S., Ramirez, J., Grigorean, G., Lebrilla, C.B.: Chiral Recognition in Gas phase Cyclodextrin: Amino Acid Complexes. J. Am. Soc. Mass Spec. 12, 278–287 (2001)
Mbamala, E.C., Pastore, G.: Optimal Monte Carlo Sampling for Simulation of Classical Fluids. Phys. A. 313, 312–320 (2002)
Bouzida, D., Kumar, S., Swendsen, R.H.: Efficient Monte Carlo Methods for the Computer Simulation of Biological Molecules. Phys. Rev. A. 45, 8894–8901 (1992)
Allen, M.P., Tildesley, D.J.: Computer Simulations of Liquids. Oxford University Press, New York (1987)
Kuttel, M., Brady, J.W., Naidoo, K.J.: Carbohydrate Solution Simulations: Producing a Force Field with Experimentally Consistent Primary Alcohol Rotational Frequencies and Populations. J. Comput. Chem. 23, 1236–1243 (2002)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Choi, Y., Kim, SR., Hwang, S., Jeong, K. (2005). A Grid Computing-Based Monte Carlo Docking Simulations Approach for Computational Chiral Discrimination. In: Ślęzak, D., Yao, J., Peters, J.F., Ziarko, W., Hu, X. (eds) Rough Sets, Fuzzy Sets, Data Mining, and Granular Computing. RSFDGrC 2005. Lecture Notes in Computer Science(), vol 3642. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11548706_47
Download citation
DOI: https://doi.org/10.1007/11548706_47
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-28660-8
Online ISBN: 978-3-540-31824-8
eBook Packages: Computer ScienceComputer Science (R0)