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Packing optimization for automated generation of complex system's initial configurations for molecular dynamics and docking

Packing optimization for automated generation of complex system's initial configurations for... Molecular Dynamics is a powerful methodology for the comprehension at molecular level of many chemical and biochemical systems. The theories and techniques developed for structural and thermodynamic analyses are well established, and many software packages are available. However, designing starting configurations for dynamics can be cumbersome. Easily generated regular lattices can be used when simple liquids or mixtures are studied. However, for complex mixtures, polymer solutions or solid adsorbed liquids (for example) this approach is inefficient, and it turns out to be very hard to obtain an adequate coordinate file. In this article, the problem of obtaining an adequate initial configuration is treated as a “packing” problem and solved by an optimization procedure. The initial configuration is chosen in such a way that the minimum distance between atoms of different molecules is greater than a fixed tolerance. The optimization uses a well‐known algorithm for box‐constrained minimization. Applications are given for biomolecule solvation, many‐component mixtures, and interfaces. This approach can reduce the work of designing starting configurations from days or weeks to few minutes or hours, in an automated fashion. Packing optimization is also shown to be a powerful methodology for space search in docking of small ligands to proteins. This is demonstrated by docking of the thyroid hormone to its nuclear receptor. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 819–825, 2003 http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Journal of Computational Chemistry Wiley

Packing optimization for automated generation of complex system's initial configurations for molecular dynamics and docking

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References (17)

Publisher
Wiley
Copyright
Copyright © 2003 Wiley Periodicals, Inc.
ISSN
0192-8651
eISSN
1096-987X
DOI
10.1002/jcc.10216
pmid
12692791
Publisher site
See Article on Publisher Site

Abstract

Molecular Dynamics is a powerful methodology for the comprehension at molecular level of many chemical and biochemical systems. The theories and techniques developed for structural and thermodynamic analyses are well established, and many software packages are available. However, designing starting configurations for dynamics can be cumbersome. Easily generated regular lattices can be used when simple liquids or mixtures are studied. However, for complex mixtures, polymer solutions or solid adsorbed liquids (for example) this approach is inefficient, and it turns out to be very hard to obtain an adequate coordinate file. In this article, the problem of obtaining an adequate initial configuration is treated as a “packing” problem and solved by an optimization procedure. The initial configuration is chosen in such a way that the minimum distance between atoms of different molecules is greater than a fixed tolerance. The optimization uses a well‐known algorithm for box‐constrained minimization. Applications are given for biomolecule solvation, many‐component mixtures, and interfaces. This approach can reduce the work of designing starting configurations from days or weeks to few minutes or hours, in an automated fashion. Packing optimization is also shown to be a powerful methodology for space search in docking of small ligands to proteins. This is demonstrated by docking of the thyroid hormone to its nuclear receptor. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 819–825, 2003

Journal

Journal of Computational Chemistry – Wiley

Published: May 1, 2003

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