title: In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation.
abstract: Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational.
authors.affiliation: The Edinburgh Parallel Computing Centre, The University of Edinburgh, Edinburgh EH9 3JZ, Scotland.
authors.forename: Alan
authors.initials: A
authors.lastname: Gray
authors.affiliation: School of Mathematics, University of Leeds, Leeds LS2 9JT, England.
authors.forename: Oliver G
authors.initials: OG
authors.lastname: Harlen
authors.affiliation: School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, England.
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Harris
authors.affiliation: Faculty of Natural and Environmental Sciences, University of Southampton, Southampton SO17 1BJ, England.
authors.forename: Syma
authors.initials: S
authors.lastname: Khalid
authors.affiliation: Faculty of Natural and Environmental Sciences, University of Southampton, Southampton SO17 1BJ, England.
authors.forename: Yuk Ming
authors.initials: YM
authors.lastname: Leung
authors.affiliation: Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
authors.forename: Richard
authors.initials: R
authors.lastname: Lonsdale
authors.affiliation: Centre for Computational Chemistry, University of Bristol, Bristol BS8 1TS, England.
authors.forename: Adrian J
authors.initials: AJ
authors.lastname: Mulholland
authors.affiliation: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England.
authors.forename: Arwen R
authors.initials: AR
authors.lastname: Pearson
authors.affiliation: School of Mathematics, University of Leeds, Leeds LS2 9JT, England.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Read
authors.affiliation: School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, England.
authors.forename: Robin A
authors.initials: RA
authors.lastname: Richardson
mesh_terms: D003198:Computer Simulation; D018360:Crystallography, X-Ray; D056004:Molecular Dynamics Simulation; D009696:Nucleic Acids / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory
chemical_list: D009696:Nucleic Acids; D011506:Proteins
keywords: biomolecular simulation; computational techniques