On Massive Calculations of Maps of Molecular Surface of Helical Proteins and Nucleic Acids

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Abstract


An approach has been developed for organizing massive calculations of the maps of a molecular surface of helical proteins and nucleic acids in the distributed computing media. Three new program codes SURFACE-2008-compact, PROT-Zcompact and DNA-RNA-Zcompact that represent modified Linux versions of codes SURFACE-2008, PROT-Z and DNA-RNA-Z were elaborated to calculate the surface maps of the helical protein molecules and the helical DNA-RNA molecules. In order to organize massive computing of a large set of molecules, the graphical interface and the input of control parameters in a dialog mode are eliminated from the SURFACE-2008, PROT-Z and DNA-RNA-Z codes. To input the control parameters and to run codes SURFACE-2008-compact, PROT-Zcompact and DNA-RNA-Zcompact, a special script-program has been implemented. For graphical presentation and further analysis of the maps obtained in such a way corresponding full versions of codes SURFACE-2008, PROT-Z and DNA-RNA-Z are used. The investigation has been supported by a grant of the RFBR 07-07-234.

O A Afanasiev

Joint Institute for Nuclear Research

Email: olegafan@jinr.ru
Лаборатория информационных технологий; Объединённый институт ядерных исследований; Joint Institute for Nuclear Research

P V Zrelov

Joint Institute for Nuclear Research

Email: zrelov@jinr.ru
Лаборатория информационных технологий; Объединённый институт ядерных исследований; Joint Institute for Nuclear Research

V V Ivanov

Joint Institute for Nuclear Research

Email: ivanov@jinr.ru
Лаборатория информационных технологий; Объединённый институт ядерных исследований; Joint Institute for Nuclear Research

V A Stepanenko

Joint Institute for Nuclear Research

Email: vstep@jinr.ru
Лаборатория информационных технологийОбъединённый институт ядерных исследований; Объединённый институт ядерных исследований; Joint Institute for Nuclear Research

R V Polozov

Institute of Theoretical and Experimental BiophysicsRussian Academy of Sciences

Email: polrob@mail.ru
Institute of Theoretical and Experimental BiophysicsRussian Academy of Sciences

Yu N Chirgadze

Institute of Protein ResearchRussian Academy of Sciences

Email: chir@vega.protres.ru
Institute of Protein ResearchRussian Academy of Sciences

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Copyright (c) 2010 Афанасьев О.А., Зрелов П.В., Иванов В.В., Степаненко В.А., Полозов Р.В., Чиргадзе Ю.Н.

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