PROTEIN DATA BANK BIOMEDICAL COMMUNITY SERVICES

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 而子项目的主要调查员可能是由其他来源提供的， 包括其它NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， 而不是由NCRR赠款提供给子项目或子项目工作人员的直接资金。 （一） 目标 RCSB蛋白质数据库（PDB）是一个国际性的三维蛋白质数据库。 大分子结构数据（Berman等人，2000年）。 RCSB团队由教授领导。 海伦伯曼，正在申请一个新的五年赠款经营PDB的过程中。 这一合作项目将使每个项目中提议的活动产生协同效应 退款因此，这两个项目将更强大，更有价值的社区， 用户比其他情况下。这一协同努力的目标如下： 每个资源： 对于PDB： + NBCR将提供一个分发和使用蛋白质功能位点搜索的工具 由PDB生成并作为Web服务提供的信息。场地法 搜索尚未确定，将由PDB在早期阶段进行评估。 退款其目的是提供类似的结合位点的细节，这些结合位点对 从进化关系到药物发现的各种研究。 + NBCR将提供一个分布式环境来支持数据的计算 与三维结构比较相关。PDB更新需要这些数据 最初由FatCat方法计算（Ye和Godzik 2004），该方法提供了 蛋白质弹性稍后将评估其他方法。在任一情况下， 全蛋白质结构比较是一项高性能任务， NBCR的基础设施。 对于NBCR： PDB将为以下服务提供高知名度和受众： + 通过将结构比较的结果和其他数据传递给应用程序 NBCR中间件。 + 为网格服务提供试验平台。 + 由NBCR提供静电数据，作为PDB服务的一部分（本 在PDB续期申请中没有提供，但被认为是有用的补充）。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. (A) OBJECTIVES The RCSB Protein Data Bank (PDB) is an international repository for three-dimensional macromolecular structure data (Berman et al., 2000). The RCSB team, directed by Prof. Helen Berman, is in the process of applying for a new five-year grant to operate the PDB. This collaborative project will synergize activities proposed in each respective projects renewal. As a result both projects will be stronger and more valuable to a community of users than would otherwise be the case. This synergistic effort has the following goals for each resource: For PDB: + NBCR will provide a vehicle to distribute and use protein functional site search information generated by the PDB and provided as a Web service. The method of site search is yet to be determined and will be evaluated by the PDB in the early stages of the renewal. The intent is to provide details of similar binding sites that have implications for a variety of studies from evolutionary relationships to drug discovery. + NBCR will provide a distributed environment to support the computation of data associated with 3-dimensional structure comparison. The PDB renewal calls for these data initially being calculated by the FatCat method (Ye and Godzik 2004) that provides for protein flexibility. Later other methods will be evaluated. In either case computation of an all-by-all protein structure comparison is a high performance task that can benefit from the NBCR infrastructure. For NBCR: PDB will provide high visibility and audience for services that include: + Passing the results of structure comparisons and other data to applications through NBCR middleware. + Provision of a testbed for grid services. + Provision by NBCR of electrostatic data to be included as part of PDB services (this provision was not in the PDB renewal application but is deemed a useful addition).