title: Grid computing and biomolecular simulation.
abstract: Biomolecular computer simulations are now widely used not only in an academic setting to understand the fundamental role of molecular dynamics on biological function, but also in the industrial context to assist in drug design. In this paper, two applications of Grid computing to this area will be outlined. The first, involving the coupling of distributed computing resources to dedicated Beowulf clusters, is targeted at simulating protein conformational change using the Replica Exchange methodology. In the second, the rationale and design of a database of biomolecular simulation trajectories is described. Both applications illustrate the increasingly important role modern computational methods are playing in the life sciences.
authors.affiliation: School of Chemistry, University of Southampton, Southampton, UK.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Woods
authors.forename: Muan Hong
authors.initials: MH
authors.lastname: Ng
authors.forename: Steven
authors.initials: S
authors.lastname: Johnston
authors.forename: Stuart E
authors.initials: SE
authors.lastname: Murdock
authors.forename: Bing
authors.initials: B
authors.lastname: Wu
authors.forename: Kaihsu
authors.initials: K
authors.lastname: Tai
authors.forename: Hans
authors.initials: H
authors.lastname: Fangohr
authors.forename: Paul
authors.initials: P
authors.lastname: Jeffreys
authors.forename: Simon
authors.initials: S
authors.lastname: Cox
authors.forename: Jeremy G
authors.initials: JG
authors.lastname: Frey
authors.forename: Mark S P
authors.initials: MS
authors.lastname: Sansom
authors.forename: Jonathan W
authors.initials: JW
authors.lastname: Essex
mesh_terms: D001704:Biopolymers / Q000032:analysis / Q000737:chemistry*; D003198:Computer Simulation; D048088:Informatics / Q000379:methods; D020407:Internet; D008432:Mathematical Computing; D008954:Models, Biological; D008956:Models, Chemical; D008958:Models, Molecular; D012107:Research Design; D012984:Software; D018511:Systems Integration
chemical_list: D001704:Biopolymers