PROTEIN DATA BANK BIOMEDICAL COMMUNITY SERVICES

蛋白质数据库生物医学社区服务

• 批准号: 8362805
• 负责人: Wilfred Wenfeng Li
• 金额: $ 4万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-05-01 至 2012-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8362805
• 关键词: Binding Sites; Biomedical Computing; Communities; Community Services; Data; Databases; Electrostatics; Environment; Funding; Goals; Grant; International; Methods; Molecular Structure; National Center for Research Resources; Principal Investigator; Process; Proteins; Research; Research Infrastructure; Resources; Services; Site; Source; Staging; Structure; Task Performances; United States National Institutes of Health; cost; drug discovery; flexibility; middleware; protein structure; repository; three dimensional structure; web services

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).

该副本是利用资源的众多研究子项目之一 由NIH/NCRR资助的中心赠款提供。对该子弹的主要支持 而且，副投影的主要研究员可能是其他来源提供的 包括其他NIH来源。 列出的总费用可能 代表subproject使用的中心基础架构的估计量， NCRR赠款不直接向子弹或副本人员提供的直接资金。 （a）目标 RCSB蛋白数据库（PDB）是三维的国际存储库 大分子结构数据（Berman等，2000）。 RCSB团队由教授指导。 海伦·伯曼（Helen Berman）正在申请新的五年赠款以操作PDB。 这个协作项目将协同每个项目中提出的活动 更新。结果，这两个项目将对一个社区的社区更强大，更有价值 用户比其他情况。这种协同努力具有以下目标 每个资源： 对于PDB： + NBCR将提供分发和使用蛋白质功能现场搜索的车辆 PDB生成的信息并作为Web服务提供。站点的方法 搜索尚未确定，并将在PDB的早期阶段评估 更新。目的是提供类似绑定站点的详细信息，这些网站对 从进化关系到药物发现的各种研究。 + NBCR将提供分布式环境以支持数据的计算 与三维结构比较有关。 PDB更新呼吁这些数据 最初是由Fatcat方法（Ye and Godzik 2004）计算的 蛋白质柔韧性。以后将评估其他方法。无论哪种情况， 全部蛋白质结构比较是一项高性能任务，可以从中受益 NBCR基础架构。 对于NBCR： PDB将为包括： +通过结构比较和其他数据的结果通过 NBCR中间件。 +为电网服务提供测试床。 +由NBCR提供的静电数据作为PDB服务的一部分（这 PRESISION不在PDB续订应用中，但被认为是有用的）。