Lipidbook | Resources | Beckstein Lab

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Lipidbook

Lipidbook

Lipidbook (lipidbook.bioch.ox.ac.uk ) is a public repository for force field parameters with a special emphasis on lipids, detergents, and similar molecules that are of interest when simulating biological membranes.1 It acts as a warehouse for parameter files that are supplied by the community.

A collection of files for one lipid is called a package and typically contains a topology building block (connectivity and partial charges), possibly additional force field parameter files to define non-standard atom types, and perhaps structure files such as a pdb of a single molecule or a pre-equilibrated bilayer patch.

The goal of Lipidbook is to provide a reliable single source of parameters in order to simplify the simulation of membranes and membrane-protein systems. Various features assist the user in evaluating the reliability of parameter sets:

  • A package is versioned in order to maintain a transparent history over parameter updates and improvements.
  • A package can (and should) be linked to the primary reference describing the parameters. Where possible, the PubMed link and doi are provided. The citation is also automatically included when a zip file of a package is downloaded.
  • All registered users can comment on packages. These comments are visible to everyone.
  • A package is linked to the name of the curator (i.e. the person who submitted the package and is the one who can edit it)
  • A copy of each version of a parameter files is always available, either from the Lipidbook server or from the WebCite® archive.
  • Each package comes with licence information, showing clearly if the package is open data or in some ways restricted.

References

1 J. Domański P. Stansfeld, M.S.P. Sansom, and O. Beckstein. Lipidbook: A public repository for force field parameters used in membrane simulations. J. Membrane Biol. 238 (2010), 255–258. doi:10.1007/s00232-010-9296-8