TY - JOUR
T1 - Lipidbook
T2 - A public repository for force-field parameters used in membrane simulations
AU - Domański, Jan
AU - Stansfeld, Phillip J.
AU - Sansom, Mark S.P.
AU - Beckstein, Oliver
PY - 2010/8
Y1 - 2010/8
N2 - 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.
AB - 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.
KW - Computer simulation
KW - Database
KW - Force-field parameter
KW - Lipid
KW - Membrane protein
UR - http://www.scopus.com/inward/record.url?scp=78650186363&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=78650186363&partnerID=8YFLogxK
U2 - 10.1007/s00232-010-9296-8
DO - 10.1007/s00232-010-9296-8
M3 - Article
C2 - 20700585
AN - SCOPUS:78650186363
SN - 0022-2631
VL - 236
SP - 255
EP - 258
JO - Journal of Membrane Biology
JF - Journal of Membrane Biology
IS - 3
ER -