CIBR: BBSRC-NSF/BIO: Next generation Protein Data Bank - FACT infrastructure with value added FAIR data supporting diverse research and education user communities.

CIBR：BBSRC-NSF/BIO：下一代蛋白质数据库 - FACT 基础设施，具有增值 FAIR 数据，支持多样化的研究和教育用户社区。

• 批准号: 2019297
• 负责人: Stephen Burley
• 金额: $ 161.2万
• 依托单位: Rutgers University New Brunswick
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-07-01 至 2023-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2019297&HistoricalAwards=false
• 关键词: CIBR; BBSRC; NSF; BIO; Next

This US RCSB Protein Data Bank (RCSB PDB)/Protein Data Bank in Europe (PDBe) collaborative project aims to improve data deposition, delivery, and management of three- dimensional (3D) macromolecular structure information stored in single global public data resource known as the Protein Data Bank (PDB). The PDB currently houses ~160,000 experimentally determined 3D structures of proteins and nucleic acids. It is managed according to the FAIR Principles on an open access basis by the Worldwide Protein Data Bank (wwPDB) partnership, which includes RCSB PDB, PDBe, Protein Data Bank Japan, and BioMagResBank. This project will transform the relatively static PDB archive into a living data resource composed of 3D structure information integrated with up-to- date annotations and metadata that relate each structure to its biochemical, cellular, or organismal context. Accurate data integration will help basic and applied researchers coming from agriculture to zoology, who are not experts in structural and computational biology, better understand and more fully utilize 3D structures in their day-to-day work in wet and dry laboratories. This new data repository will also enable 3D structural comparisons of proteins from different with similar or identical biochemical and biological functions thereby improving our understanding of protein evolution at the atomic level. The wwPDB maintains an information portal describing PDB global resources at https://www.wwpdb.org.The project addresses significant software engineering challenges, resulting from growth in the number and size/complexity of newly deposited macromolecular crystallography (MX) and single-particle cryo-electron microscopy (3DEM) structures, and the need to manage groups of related structures coming from serial femtosecond X-ray crystallography (SFX) using X-ray Free Electron Lasers (XFEL) and 3DEM. The project will improve the fidelity and completeness of 3D structure data deposited into the PDB by harvesting data automatically from structure determination software packages, and streamlining the wwPDB data deposition, validation, and biocuration system known as OneDep. The project will improve the accessibility of PDB data for researchers, educators, and students by extending chemical metadata for small-molecule ligands (e.g., bound cofactors and inhibitors), incorporating enhanced descriptions of macromolecular assemblies, grouping related PDB structures into investigations for more efficient, parallel data delivery; and creating a “Next Generation” PDB data repository with up-to-date metadata. Finally, the project will modernize wwPDB information technology infrastructure to futureproof PDB data management and weekly PDB archive release to the public domain by developing new application programming interfaces (APIs) and microservices infrastructure, and updating existing mechanisms for synchronization of data and software across wwPDB data centers in the US, Europe, and Asia. This work will directly benefit researchers, educators, and their students across the natural, physical, and engineering sciences.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

美国RCSB蛋白质数据库(RCSB PDB)/欧洲蛋白质数据库（PDBe）合作项目旨在改善存储在单一全球公共数据资源（称为蛋白质数据库（PDB））中的三维（3D）大分子结构信息的数据沉积，传递和管理。PDB目前容纳了约160,000个实验确定的蛋白质和核酸的3D结构。它是由全球蛋白质数据库（wwPDB）合作伙伴根据公平原则在开放获取的基础上进行管理的，该合作伙伴包括RCSB PDB、PDBe、日本蛋白质数据库和BioMagResBank。该项目将把相对静态的PDB档案转换为一个由3D结构信息组成的动态数据资源，该信息集成了最新的注释和元数据，这些注释和元数据将每个结构与其生物化学、细胞或有机环境联系起来。准确的数据集成将帮助从农业到动物学的基础和应用研究人员，他们不是结构和计算生物学的专家，更好地理解和更充分地利用3D结构在干湿实验室的日常工作中。这个新的数据存储库还将使来自不同的具有相似或相同生化和生物学功能的蛋白质的3D结构比较成为可能，从而提高我们在原子水平上对蛋白质进化的理解。wwPDB维护着一个描述PDB全球资源的信息门户网站https://www.wwpdb.org.The项目解决了重大的软件工程挑战，这些挑战来自于新沉积的大分子晶体学（MX）和单粒子冷冻电子显微镜（3DEM）结构的数量和尺寸/复杂性的增长。以及使用x射线自由电子激光器（XFEL）和3DEM管理来自连续飞秒x射线晶体学（SFX）的相关结构组的需求。该项目将通过从结构确定软件包中自动收集数据，并简化wwPDB数据沉积、验证和生物固化系统（OneDep），提高沉积到PDB中的3D结构数据的保真度和完整性。该项目将通过扩展小分子配体（例如，结合辅因子和抑制剂）的化学元数据，结合大分子组装的增强描述，将相关的PDB结构分组到调查中，以提高PDB数据的可访问性，为研究人员、教育工作者和学生改善PDB数据的可访问性；并创建具有最新元数据的“下一代”PDB数据存储库。最后，该项目将通过开发新的应用程序编程接口（api）和微服务基础设施，以及更新现有的跨美国、欧洲和亚洲的wwPDB数据中心的数据和软件同步机制，使wwPDB信息技术基础设施现代化，以实现面向未来的PDB数据管理和每周向公共领域发布PDB存档。这项工作将直接使自然、物理和工程科学领域的研究人员、教育工作者及其学生受益。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。