Grid and distributed public computing schemes for structural proteomics: a short overview

  • Authors:

  • Azhar Ali Shah;Daniel Barthel;Natalio Krasnogor

  • Affiliations:

  • School of Computer Science and Information Technology, University of Nottingham, UK;School of Computer Science and Information Technology, University of Nottingham, UK;School of Computer Science and Information Technology, University of Nottingham, UK

  • Venue:
  • ISPA'07 Proceedings of the 2007 international conference on Frontiers of High Performance Computing and Networking
  • Year:
  • 2007

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Abstract

Grid and distributed public computing schemes has become an essential tool for many scientific fields including bioinformatics, computational biology and systems biology. The adoption of these technologies has given rise to a wide range of projects and contributions that provide various ways of setting up these environments and exploiting their potential resources and services for different domains of applications. This paper aims to provide a distilled overview of some of the major projects, technologies and resources employed in the area of structural proteomics. The major emphasis would be to briefly comment on various approaches related to the gridification and parallelization of some flagship legacy applications, tools and data resources related to key structural proteomics problems such as protein structure prediction, folding and comparison. The comments are based on theoretical analysis of some interesting parameters such as performance gain after gridification, user level interaction environments, workload distribution and the choice of deployment infrastructure and technologies. The study of these parameters would provide a basis for some motivating justification needed for further research and development in this domain.