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Quality assurance for biomolecular simulations

Murdock, Stuart E., Tai, Kaihsu, Ng, Muan Hong, Johnston, Steven, Wu, Bing, Fangohr, Hans, Laughton, Charles A., Essex, Jonathan W and Sansom, Mark S.P. (2006) Quality assurance for biomolecular simulations Journal of Chemical Theory and Computation, 2, (6), pp. 1477-1481. (doi:10.1021/ct6001708).

Record type: Article

Abstract

Contemporary structural biology has an increased emphasis on high- throughput methods. Biomolecular simulations can add value to structural biology via the provision of dynamic information. However, at present there are no agreed measures for the quality of biomolecular simulation data. In this Letter, we suggest suitable measures for the quality assurance of molecular dynamics simulations of biomolecules. These measures are designed to be simple, fast, and general. Reporting of these measures in simulation papers should become an expected practice, analogous to the reporting of comparable quality measures in protein crystallography. We wish to solicit views and suggestions from the simulation community on methods to obtain reliability measures from molecular- dynamics trajectories. In a database which provides access to previously obtained simulations-for example BioSimGrid (http://www.biosimgrid.org/)-the user needs to be confident that the simulation trajectory is suitable for further investigation. This can be provided by the simulation quality measures which a user would examine prior to more extensive analyses.

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More information

Published date: 2006
Keywords: dynamics, validation, proteins

Identifiers

Local EPrints ID: 44507
URI: http://eprints.soton.ac.uk/id/eprint/44507
ISSN: 1549-9618
PURE UUID: 4a0ab5f5-4614-4209-8ab0-d1f697a61dcb
ORCID for Steven Johnston: ORCID iD orcid.org/0000-0003-3864-7072
ORCID for Jonathan W Essex: ORCID iD orcid.org/0000-0003-2639-2746

Catalogue record

Date deposited: 02 Mar 2007
Last modified: 17 Jul 2017 15:14

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Contributors

Author: Stuart E. Murdock
Author: Kaihsu Tai
Author: Muan Hong Ng
Author: Steven Johnston ORCID iD
Author: Bing Wu
Author: Hans Fangohr
Author: Charles A. Laughton
Author: Mark S.P. Sansom

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