Lipidbook: A public repository for force-field parameters used in membrane simulations

Jan Domański, Phillip J. Stansfeld, Mark S.P. Sansom, Oliver Beckstein

Research output: Contribution to journalArticle

113 Scopus citations

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, parametersand 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 ofmechanisms are implemented to aid a user in judging the appropriateness of a given parameter set for a project. For nstance, 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 dataare 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, thusensuring 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.

Original languageEnglish (US)
Pages (from-to)255-258
Number of pages4
JournalJournal of Membrane Biology
Volume236
Issue number3
DOIs
StatePublished - Aug 1 2010

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Keywords

  • Computer simulation
  • Database
  • Force-field parameter
  • Lipid
  • Membrane protein

ASJC Scopus subject areas

  • Biophysics
  • Physiology
  • Cell Biology

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