PROTEIN DATA BANK BIOMEDICAL COMMUNITY SERVICES

这个子项目是利用资源的许多研究子项目之一。 由NIH/NCRR资助的中心拨款提供。对子项目的主要支持 子项目的首席调查员可能是由其他来源提供的， 包括美国国立卫生研究院的其他来源。为子项目列出的总成本可能 表示该子项目使用的中心基础设施的估计数量， 不是由NCRR赠款提供给次级项目或次级项目工作人员的直接资金。 (A)目标 RCSB蛋白质数据库(PDB)是一个国际三维数据库 大分子结构数据(Berman等人，2000年)。RCSB团队，由RCSB教授指导。 海伦·伯曼正在申请新的为期五年的拨款，以运营PDB。 该合作项目将协同每个项目中提出的活动。 更新。因此，这两个项目将更加强大，对 用户比其他情况下更多。这一协同努力有以下目标 每种资源： 对于PDB： +NBCR将提供一种传播和使用蛋白质功能站点搜索的工具 由PDB生成并作为Web服务提供的信息。选址方法 搜寻工作尚待确定，并将由临时局在 更新。其目的是提供类似结合位点的详细信息，这些结合位点对 从进化关系到药物发现的各种研究。 +NBCR将提供分布式环境来支持数据计算 与三维结构比较相关联。PDB续订需要这些数据 最初是由FatCat方法(Ye和Godzik 2004)计算的，该方法规定 蛋白质的灵活性。稍后将对其他方法进行评估。在这两种情况下，都会计算 全面的蛋白质结构比较是一项高性能的任务，可以受益于 NBCR基础设施。 对于NBCR： PDB将为以下服务提供较高的可见性和受众： +通过将结构比较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床。 +NBCR将静电数据作为PDB服务的一部分提供(此 PDB续签申请中没有规定，但被认为是一项有用的补充)。

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).