Mathematical Biology & Bioinformatics | Volume 12 Issue 2 Year 2017

Mass Calculations of Electrostatic Potentials and Molecular Surface Maps of Proteins and Nucleic Acids in a Distributed Computer Environment: Workflow and Algorithms

Akishina T.P., Grokhlina T.I., Zrelov P.V., Ivanov V.V., Polozov R.V., Sivozhelezov V.S., Stepanenko V.A., Chirgadze Yu.N., Yakovlev A.V.

Joint Institute for Nuclear Research, Dubna, Russia
Institute of Mathematical Problems of Biology, the Keldysh Institute of Applied Mathematics RAS, Pushchino, Russia
National Research Nuclear University ”MEPhI”, Moscow, Russia
Institute of Theoretical and Experimental Biophysics, RAS, Puschino, Russia
Institute of Cell Biophysics, RAS, Puschino, Russia
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.