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

dc.creatorMartinez, JM
dc.creatorMartinez, L
dc.date2003
dc.dateMAY
dc.date2014-11-19T04:22:15Z
dc.date2015-11-26T17:02:00Z
dc.date2014-11-19T04:22:15Z
dc.date2015-11-26T17:02:00Z
dc.date.accessioned2018-03-28T23:49:59Z
dc.date.available2018-03-28T23:49:59Z
dc.identifierJournal Of Computational Chemistry. John Wiley & Sons Inc, v. 24, n. 7, n. 819, n. 825, 2003.
dc.identifier0192-8651
dc.identifierWOS:000182499000003
dc.identifier10.1002/jcc.10216
dc.identifierhttp://www.repositorio.unicamp.br/jspui/handle/REPOSIP/58983
dc.identifierhttp://www.repositorio.unicamp.br/handle/REPOSIP/58983
dc.identifierhttp://repositorio.unicamp.br/jspui/handle/REPOSIP/58983
dc.identifier.urihttp://repositorioslatinoamericanos.uchile.cl/handle/2250/1278824
dc.descriptionMolecular 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. (C) 2003 Wiley Periodicals, Inc.
dc.description24
dc.description7
dc.description819
dc.description825
dc.languageen
dc.publisherJohn Wiley & Sons Inc
dc.publisherHoboken
dc.publisherEUA
dc.relationJournal Of Computational Chemistry
dc.relationJ. Comput. Chem.
dc.rightsfechado
dc.rightshttp://olabout.wiley.com/WileyCDA/Section/id-406071.html
dc.sourceWeb of Science
dc.subjectlarge-scale optimization
dc.subjectbox constraints
dc.subjectmolecular dynamics
dc.subjectdocking
dc.subjectBox Constraints
dc.subjectAlgorithm
dc.subjectEnergy
dc.subjectMinimization
dc.subjectSimulation
dc.subjectPrograms
dc.subjectSet
dc.titlePacking optimization for automated generation of complex system's initial configurations for molecular dynamics and docking
dc.typeArtículos de revistas


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