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JOURNALS // Matematicheskaya Biologiya i Bioinformatika // Archive

Mat. Biolog. Bioinform., 2017 Volume 12, Issue 2, Pages 354–374 (Mi mbb299)

Information and Computing Technologies in Biology and Medicine

Mass calculations of electrostatic potentials and molecular surface maps of proteins and nucleic acids in a distributed computer environment: workflow and algorithms

T. P. Akishinaa, T. I. Grokhlinab, P. V. Zrelova, V. V. Ivanovca, R. V. Polozovd, V. S. Sivozhelezove, V. A. Stepanenkoa, Yu. N. Chirgadzef, A. V. Yakovleva

a Joint Institute for Nuclear Research, Dubna, Russia
b Institute of Mathematical Problems of Biology, the Keldysh Institute of Applied Mathematics RAS, Pushchino, Russia
c National Research Nuclear University ”MEPhI”, Moscow, Russia
d Institute of Theoretical and Experimental Biophysics, RAS, Puschino, Russia
e Institute of Cell Biophysics, RAS, Puschino, Russia
f Institute of Protein Research, RAS, Puschino, Russia

Abstract: The two key factors determining processes of transcription and translation within each single cell are the distributions of electrostatic potential, and the molecular surface structures of nucleic acids, of transcription factors, and of their complexes. However, calculations of electrostatic potentials and molecular surface maps are time consuming and require too much computer resources. To resolve the issues, we have developed a technology and a software for calculations in a distributed computational media containing thousands of processor cores.

Key words: DNA, RNA, proteins, transcription factors, electrostatic potential, molecular-surface maps, mass calculations, distributed computing environment.

UDC: 123.4

Received 01.10.2017, Published 30.10.2017

DOI: 10.17537/2017.12.354



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