| MDTRA: A molecular dynamics trajectory analyzer with a graphical user interface. | |
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MedLine Citation:
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PMID: 23047307 Owner: NLM Status: Publisher |
Abstract/OtherAbstract:
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Most of existing software for analysis of molecular dynamics (MD) simulation results is based on command-line, script-guided processes that require the researchers to have an idea about programming language constructions used, often applied to the one and only product. Here, we describe an open-source cross-platform program, MD Trajectory Reader and Analyzer (MDTRA), that performs a large number of MD analysis tasks assisted with a graphical user interface. The program has been developed to facilitate the process of search and visualization of results. MDTRA can handle trajectories as sets of protein data bank files and presents tools and guidelines to convert some other trajectory formats into such sets. The parameters analyzed by MDTRA include interatomic distances, angles, dihedral angles, angles between planes, one-dimensional and two-dimensional root-mean-square deviation, solvent-accessible area, and so on. As an example of using the program, we describe the application of MDTRA to analyze the MD of formamidopyrimidine-DNA glycosylase, a DNA repair enzyme from Escherichia coli. © 2012 Wiley Periodicals, Inc. |
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Authors:
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Alexander V Popov; Yury N Vorobjev; Dmitry O Zharkov |
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Publication Detail:
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Type: JOURNAL ARTICLE Date: 2012-10-10 |
Journal Detail:
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Title: Journal of computational chemistry Volume: - ISSN: 1096-987X ISO Abbreviation: J Comput Chem Publication Date: 2012 Oct |
Date Detail:
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Created Date: 2012-10-10 Completed Date: - Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 9878362 Medline TA: J Comput Chem Country: - |
Other Details:
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Languages: ENG Pagination: - Citation Subset: - |
Copyright Information:
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Copyright © 2012 Wiley Periodicals, Inc. |
Affiliation:
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SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia. apopov@niboch.nsc.ru. |
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