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

O A Afanasiev; Афанасьев Олег Александрович; P V Zrelov; Зрелов Пётр Валентинович; V V Ivanov; Иванов Виктор Владимирович; V A Stepanenko; Степаненко Виктор Алексеевич; R V Polozov; Полозов Роберт Валентинович; Yu N Chirgadze; Чиргадзе Юрий Николаевич

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

Authors: Afanasiev OA¹, Zrelov PV¹, Ivanov VV¹, Stepanenko VA¹, Polozov RV², Chirgadze Y.N³
Affiliations:
1. Joint Institute for Nuclear Research
2. Institute of Theoretical and Experimental BiophysicsRussian Academy of Sciences
3. Institute of Protein ResearchRussian Academy of Sciences
Issue: No 3.2 (2010)
Pages: 72-76
Section: Articles
URL: https://journals.rudn.ru/miph/article/view/8509

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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.

Keywords

distributed computing systems, helical proteins, nucleic acids, mapping, script-program

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Vol 32, No 2 (2024)

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

Full Text

Abstract

Keywords

About the authors

O A Afanasiev

P V Zrelov

V V Ivanov

V A Stepanenko

R V Polozov

Yu N Chirgadze

References

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