About BioSimGrid

The aim of the BioSimGrid project is to make the results of large-scale computer simulations of biomolecules more accessible to the biological community. Such simulations of the motions of proteins are a key component in understanding how the structure of a protein is related to its dynamic function.

Summary

Modern biology requires new approaches to biomolecular simulation. With nearly 200 000 protein sequences in the genomic databases, and over 33 000 structures deposited in the Protein Data Bank, single simulations of a single protein do not address the needs of contemporary biology. We are developing tools that will enable biomolecular simulations to provide an essential link between structural genomics and systems biology. In particular, the simulation community has to addressing three key areas of simulation technology: high-throughput simulations for high-performance computing, a grid-enabled database for comparative analysis of simulation data, and multi-scale biomolecular simulations ranging from the quantum-mechanical to the meso-scale. That is, we need to be ready to provide both the computational infrastructure and pharmaceutically relevant test cases to demonstrate the validity of this new approach. BioSimGrid, as a distributed database for biomolecular simulations, provides the keystone in the endeavour.

Collaborators

• University of Oxford
  • Mark Sansom, Biochemistry
  • Paul Jeffreys, e-Science
  • Kaihsu Tai, Biochemistry
  • Bing Wu, Biochemistry and e-Science (alumnus)
  • Syma Khalid, Biochemistry
• University of Southampton
  • Jonathan Essex, Chemistry
  • Simon Cox, e-Science
  • Hans Fangohr, e-Science
  • Stuart Murdock, Chemistry and e-Science (alumnus)
  • Muan Hong Ng, e-Science
  • Steven Johnston, Chemistry and e-Science
  • Richard Boardman, Chemistry and e-Science
• Elsewhere in the United Kingdom
  • David Moss, Birkbeck, London
  • Adrian Mulholland, Bristol
  • Charles Laughton, Nottingham
  • Leo Caves, York
• Collaborators worldwide
  • Tjerk Straatsma, Pacific Northwest National Laboratory, Richland, Washington, USA (research highlight: New grid aligns world-class researchers)
  • J. Andrew McCammon, University of California, San Diego, La Jolla, California, USA
  • Jesús Izaguirre, University of Notre Dame, South Bend, Indiana, USA

Acknowledgements

This project is funded by BBSRC (Biology and e-Science) and DTI (e-Science Pilot Projects), and supported by the Oxford e-Science Centre and the Southampton Regional e-Science Centre. Additional support is provided by the Worldwide Universities Network.