VIRTUAL LABORATORY MOLDYNGRID AS A PART OF SCIENTIFIC INFRASTRUCTURE FOR BIOMOLECULAR SIMULATIONS
DOI:
https://doi.org/10.47839/ijc.9.4.721Keywords:
Grid, virtual laboratory, molecular dynamics, GROMACS, web-portal.Abstract
Virtual laboratory MolDynGrid has been established for computational researches in structural biology and bioinformatics, especially for molecular dynamics (MD) simulations of biological macromolecules and their complexes. Biomolecular simulation usually requires a very high processing power and huge storage space for MD trajectories. In this study we describe the development of virtual laboratory infrastructure to run massive MD simulations on a Grid infrastructure in a distributed manner. The aim of MolDynGrid development was to provide an efficient infrastructure for automation of MD job processing in Grid. It will assist researchers to use grid technology without having them to be familiar with highly complicated internals of the Grid. Web-portal of MolDynGrid virtual laboratory has been developed (http://moldyngrid.org), which consists of computational, analytical and educational blocks аnd data base of MD simulations.References
J. Norberg, L. Nilsson. Advances in biomolecular simulations: methodology and recent applications. Quot. Rev. Biophys. (36) (2003). pp. 257-306.
M. Karplus, J. A. McCammon. Molecular dynamics simulations of biomolecules. Nature Structural Biology (9) (2002). pp. 646-652.
D. Kovalskyy, V. Dubyna, A. E. Mark, A. Kornelyuk. A molecular dynamics study of the structural stability of HIV-1 protease under physiological conditions: The role of Na+ ions in stabilizing the active site. Proteins (58) (2005). pp. 450-458.
F. Gagliardi, B. Jones, F. Grey, M. E. Begin, M. Heikkurinen. Building an infrastructure for scientific Grid computing: status and goals of the EGEE project. Philos Transact A Math Phys. Eng. Sci. 363 (1833) (2005). pp. 1729-1742.
L. Milanesi, I. Merelli. High performance Grid based implementation for genomics and protein analysis. Stud Health Technol Inform. (120) (2006). pp. 374-380.
B. G. Kim, N. D. Nhan, S. Lee, S. Hwang, B. Breton. DrugScreener-G: towards an integrated environment for Grid-enabled large-scale virtual screening and drug discovery. Fourth IEEE International Conference on eScience (2008). pp. 666-671.
A. I. Kornelyuk, О. P. Mintser. Modern computational Grid-technologies and their applications in medical researches. Medical Informatics and Engineering 1 (1) (2008). pp. 23-29.
L. Milanesi, I. Merelli. High performance GRID based implementation for genomics and protein analysis. Stud. Health Technol. Inform. (120) (2006). pp. 374-380.
B. Wu. A Web. Grid portal implementation of BioSimGrid: a biomolecular simulation database. B. Wu, D. Matthew, et al. http://eprints.soton.ac.uk/22809/01/Wu_04.pdf: University of Southampton and University of Oxford, 2004.-March 31.
M. Zynovyev, S. Svistunov, O. Sudakov, Yu. Boyko. Ukrainian Grid infrastructure: practical experience. Proceedings of 4-th IEEE Workshop IDAACS 2007, Dortmund, Germany 6-8 September 2007, рp. 165-169.
A. O. Salnikov, I. A. Sliusar, O. O. Sudakov, Yu. V. Boyko, A. I. Kornelyuk. Implementing the file storage system in the ukrainian academic Grid infrastructure. Abstracts of 21th International CODATA Conference “Scientific Information for Society-from Today to the Future, Kyiv, Ukraine 5-8 October 2008, p. 31.
D. Van Der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, H. J. Berendsen. GROMACS: fast, flexible and free. J. Comput. Chem. (26) (2005). pp. 1701-1718.
A. O. Salnikov, I. A. Sliusar, O. O. Sudakov, Yu. V. Boyko. Ukrainian GRID-segment authorization system. Proceedings, III International Conference “Electronics and Applied Physics”, Kyiv, Ukraine 25-27 October 2007, p. 163.
gLite 3.1 home page, 2008. http://glite.org
M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Raiteri, D. Donadio, F. Marinelli, F. Pietrucci, R. A. Broglia and M. Parrinello. PLUMED: a portable plugin for free energy calculations with molecular dynamics. Comp. Phys. Comm. (180) (2009). p.1961.
A. O. Salnikov, I. A. Sliusar, O. O. Sudakov, O. V. Savytskyi, A. I. Kornelyuk. MolDynGrid virtual laboratory as a part of Ukrainian academic Grid infrastructure. Proceedings of the 5-th IEEE Workshop IDAACS 2009, Rende (Cosenza), Italy 21-23 September 2009, pp. 237-240.
Ukrainian academic Grid community, 2010. http://grid.bitp.kiev.ua
O. O. Sudakov, Yu. V. Boyko, T. V. Necheporuk, T. P. Korotkova. Performance optimization of computing cluster with weakly interconnected components. Mathematical Machines and Systems. – 2004. – N 4. – Р. 57–65.
Downloads
Published
How to Cite
Issue
Section
License
International Journal of Computing is an open access journal. Authors who publish with this journal agree to the following terms:• Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
• Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
• Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work.
