Lipidbook: A Public Repository for Force-Field Parameters Used in Membrane Simulations
Lipidbook: A Public Repository for Force-Field Parameters Used in Membrane Simulations
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DOI：
10.1007/s00232-010-9296-8
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发表时间：
2010-08-01
影响因子：
2.4
通讯作者：
Beckstein, Oliver
中科院分区：
文献类型：
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作者：
Domanski, Jan;Stansfeld, Phillip J.;Beckstein, Oliver
Lipidbook是一个力场参数的公共数据库，特别强调模拟生物膜系统时感兴趣的脂质，洗涤剂和类似分子。它存储社区提供的参数文件。拓扑结构、参数和脂质或整个双层结构可以以任何格式存放用于任何模拟代码，优选地在促进“开放知识”的许可下。“实施了许多机制来帮助用户判断给定参数集对项目的适当性。例如，参数集是版本化的，通过PubMed标识符和数字对象标识符（DOI）链接到主要引文，用户可以公开评论存放的参数。许可证发放以及使用和传播学术产生的数据的条件往往不明确。在这些情况下，也可以提供链接而不是上传文件。然后使用WebCite（A（R））服务将链接文件的快照存档，而无需用户或Lipidbook的进一步参与，从而确保参数集的透明和永久历史。Lipidbook可以在http://lipidbook.bioch.ox.ac.uk上免费访问。
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(A (R)) 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.