About

Lipidbook 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. It acts as a warehouse for parameter files that are supplied by the community. Anyone can browse and download parameters but deposition of files requires user registration.

database browser

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.

As a matter of established academic standards, Lipidbook urges users to always cite the corresponding primary reference for a parameter set to attribute full credit to the author(s) of the parameters.

Our Policy describes the terms under which data are made available and how we are dealing with your personal information.

Note that the operators of this website do not guarantee that the content made available via Lipidbook is correct or suitable for any purpose. It is the user's responsibility to verify that the parameters are producing sensible results.

Please read all referenced literature, the package abstract, and comments on the package from other users and judge for yourself.

Archival of links instead of files through WebCite®

Users on Lipidbook can add links to parameter files on other web pages instead of uploading the files. In order to maintain accessible and accurate versions of these files, Lipidbook inititates a WebCite® archival request and then links to the snapshot of the file archived on www.webcitation.org instead of the original URL. The original URL is still displayed on Lipidbook.

For a more detailed discussion see our WebCite/Lipidbook FAQ. Please contact us if you have any concerns regarding linking to or archival of your files.

Bug reporting and feature requests

Please report bugs and requests for improvements through our Issue Tracking System. You will have to register separately with a valid email address (and we apologize for the inconvenience).

Thank you!

Credits and Funding

The website and database were written by Jan Domański <> under supervision of Oliver Beckstein and Mark S. P. Sansom.

Lipidbook is described in

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. 236 (2010), 255—258. doi:10.1007/s00232-010-9296-8. URL:http://lipidbook.bioch.ox.ac.uk

preprint (pdf)

The site is implemented with the symfony web framework on top of a mySQL database. It relies on WebCite® for archival of links to parameter files.

Development was supported by a grant from the Wellcome Trust, with additional funding from the EDICT project and BBSRC.

The Wellcome Trust EDICT BBSRC

Contact

SBCB

Lipidbook is hosted in the Structural Bioinformatics and Computational Biochemistry Unit at the Department of Biochemistry in the University of Oxford.

In case of concerns, questions or problems please contact the current Lipidbook Maintainer <>, or either Dr. Oliver Beckstein <> or Prof. Mark Sansom <>.