Quality assurance for biomolecular simulations
Quality assurance for biomolecular simulations
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.
dynamics, validation, proteins
1477-1481
Murdock, Stuart E.
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Tai, Kaihsu
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Ng, Muan Hong
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Johnston, Steven
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Wu, Bing
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Fangohr, Hans
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Laughton, Charles A.
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Essex, Jonathan W
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Sansom, Mark S.P.
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2006
Murdock, Stuart E.
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Tai, Kaihsu
363c10d0-8583-4bea-bc0f-5be75142e5de
Ng, Muan Hong
6cdc5c67-aaa2-4153-b64c-3491ad848fce
Johnston, Steven
6b903ec2-7bae-4a56-9c21-eea0a70bfa2b
Wu, Bing
68da5cb1-6a5f-46f9-8173-12d702625220
Fangohr, Hans
9b7cfab9-d5dc-45dc-947c-2eba5c81a160
Laughton, Charles A.
0a484097-8092-443e-bc0b-5fec1c16ca45
Essex, Jonathan W
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Sansom, Mark S.P.
ed30b4fc-bc73-4ad7-8c56-f51a67136e4e
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), .
(doi:10.1021/ct6001708).
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.
Text
Murd_06.pdf
- Accepted Manuscript
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["date_types_typename_published" not defined] 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
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Date deposited: 02 Mar 2007
Last modified: 16 Mar 2024 03:09
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Contributors
Author:
Stuart E. Murdock
Author:
Kaihsu Tai
Author:
Muan Hong Ng
Author:
Bing Wu
Author:
Charles A. Laughton
Author:
Mark S.P. Sansom
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