PROTEIN DATA BANK BIOMEDICAL COMMUNITY SERVICES

蛋白质数据库生物医学社区服务

• 批准号: 7955293
• 负责人: Helen M Berman
• 金额: $ 0.32万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-05-01 至 2010-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7955293
• 关键词: Binding Sites; Biomedical Computing; Communities; Community Services; Computer Retrieval of Information on Scientific Projects Database; Data; Databases; Electrostatics; Environment; Funding; Goals; Grant; Institution; International; Internet; Methods; Molecular Structure; Process; Proteins; Research; Research Infrastructure; Research Personnel; Resources; Services; Site; Source; Staging; Structure; Task Performances; United States National Institutes of Health; drug discovery; flexibility; middleware; protein structure; repository; three dimensional structure

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. (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).

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 （一） 目标 RCSB蛋白质数据库（PDB）是三维大分子结构数据的国际储存库（Berman等人，2000年）。 由Helen Berman教授领导的RCSB团队正在申请一项新的五年拨款来运营PDB。这一合作项目将使每一个项目延期中提议的活动产生协同效应。因此，这两个项目将比其他情况下更强大，对用户社区更有价值。这种协同努力对每种资源都有以下目标： 对于PDB： + NBCR将提供一种工具来分发和使用PDB生成的蛋白质功能站点搜索信息，并作为Web服务提供。至于选址方法，则有待决定，并会由临时发展局在续期初期作出评估。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都有影响。 + NBCR将提供一个分布式环境来支持与三维结构比较相关的数据计算。PDB更新要求这些数据最初通过提供蛋白质灵活性的FatCat方法（Ye和Godzik 2004）计算。稍后将评估其他方法。在任何一种情况下，逐个蛋白质结构比较的计算都是一项高性能任务，可以从NBCR基础设施中受益。 对于NBCR： PDB将为以下服务提供高知名度和受众： + 通过NBCR中间件将结构比较的结果和其他数据传递给应用程序。 + 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（该规定不在PDB更新申请中，但被视为有用的补充）。