Lipidbook: A Public Repository for Force-Field Parameters Used in Membrane Simulations

Lipidbook: A Public Repository for Force-Field Parameters Used in Membrane Simulations Lipidbook is a public database for force-field parameters with a special emphasis on lipids, detergents and similar molecules that are of interest when simulating biological membrane systems. It stores parameter files that are supplied by the community. Topologies, parameters and lipid or whole bilayer structures can be deposited in any format for any simulation code, preferably under a license that promotes “open knowledge.” A number of mechanisms are implemented to aid a user in judging the appropriateness of a given parameter set for a project. For instance, parameter sets are versioned, linked to the primary citation via PubMed identifier and digital object identifier (DOI), and users can publicly comment on deposited parameters. Licensing and, hence, the conditions for use and dissemination of academically generated data are often unclear. In those cases it is also possible to provide a link instead of uploading a file. A snapshot of the linked file is then archived using the WebCite® service without further involvement of the user or Lipidbook, thus ensuring a transparent and permanent history of the parameter set. Lipidbook can be accessed freely online at http://lipidbook.bioch.ox.ac.uk . Deposition of data requires online registration. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png The Journal of Membrane Biology Springer Journals

Lipidbook: A Public Repository for Force-Field Parameters Used in Membrane Simulations

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Publisher
Springer-Verlag
Copyright
Copyright © 2010 by Springer Science+Business Media, LLC
Subject
Life Sciences; Human Physiology ; Biochemistry, general
ISSN
0022-2631
eISSN
1432-1424
D.O.I.
10.1007/s00232-010-9296-8
Publisher site
See Article on Publisher Site

Abstract

Lipidbook is a public database for force-field parameters with a special emphasis on lipids, detergents and similar molecules that are of interest when simulating biological membrane systems. It stores parameter files that are supplied by the community. Topologies, parameters and lipid or whole bilayer structures can be deposited in any format for any simulation code, preferably under a license that promotes “open knowledge.” A number of mechanisms are implemented to aid a user in judging the appropriateness of a given parameter set for a project. For instance, parameter sets are versioned, linked to the primary citation via PubMed identifier and digital object identifier (DOI), and users can publicly comment on deposited parameters. Licensing and, hence, the conditions for use and dissemination of academically generated data are often unclear. In those cases it is also possible to provide a link instead of uploading a file. A snapshot of the linked file is then archived using the WebCite® service without further involvement of the user or Lipidbook, thus ensuring a transparent and permanent history of the parameter set. Lipidbook can be accessed freely online at http://lipidbook.bioch.ox.ac.uk . Deposition of data requires online registration.

Journal

The Journal of Membrane BiologySpringer Journals

Published: Aug 11, 2010

References

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