CIBR 19-BBSRC-NSF/BIO: Next generation PDB - FACT infrastructure with value added FAIR data supporting diverse research and education user communities

CIBR 19-BBSRC-NSF/BIO：下一代 PDB - 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: BB/V004247/1
• 负责人: Sameer Velankar
• 金额: $ 48.28万
• 依托单位: European Bioinformatics Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2021
• 资助国家: 英国
• 起止时间: 2021 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FV004247%2F1
• 关键词: CIBR; 19; BBSRC; NSF; BIO

The vision of this US RCSB Protein Data Bank/Protein Data Bank in Europe collaborative project is to improve data deposition, delivery, and management of three-dimensional (3D) macromolecular structure information stored in the Protein Data Bank. This work will benefit researchers, educators, and their students across the natural, physical, and engineering sciences."Form (meaning shape/3D structure) dictates function in biology" - was first revealed in the Watson and Crick publication of the DNA double helix structure. Since their landmark discovery, interdisciplinary collaborative teams of biologists, physicists, chemists, and engineers have generated ~160,000 experimentally determined 3D structures of proteins and nucleic acids, which are centrally stored in a public data resource known as the Protein Data Bank (PDB). Founded in 1971 as the first open-access digital data resource in biology, the PDB has grown more than 20,000-fold to become the single global archive housing richly annotated 3D structures of proteins and DNA and RNA. This public-domain 3D structure data resource has had an enormous impact on fundamental biology, biomedicine, biotechnology, and bioenergy by enabling atomic-level understanding of naturally-occurring and engineered biomolecule, and by facilitating discovery of nearly 90% of the new drugs approved by the United States (US) Food and Drug Administration between 2010-2016. Today, new PDB structures are coming from macromolecular crystallography (MX), nuclear magnetic resonance spectroscopy (NMR), single-particle cryo-electron microscopy (3DEM), and micro-crystal electron diffraction (microED). X-ray free electron lasers and new integrative methods for structure determination are accelerating biomedical research with insights into ever more complex biological systems at the atomic level. Cryo-electron tomography even allows studies of macromolecular machines "caught in the act" inside frozen cells.Since 2003, the Worldwide Protein Data Bank (wwPDB, wwpdb.org) partnership has managed the PDB Core Archive (hereafter PDB archive) as a global Public Good according to the FACT principles of Fairness-Accuracy-Confidentiality-Transparency and the FAIR principles of Findability-Accessibility-Interoperability-Reusability. The wwPDB includes locally-funded partners in the US (Research Collaboratory for Structural Bioinformatics Protein Data Bank, RCSB PDB), Europe (Protein Data Bank in Europe, PDBe) and Asia (Protein Data Bank Japan, PDBj), plus a specialist NMR resource (BioMagResBank, BMRB). The wwPDB also enables equitable sharing of PDB data archiving and management costs between US, Europe, and Asia. In 2019, RCSB PDB, PDBe, and PDBj jointly processed 13,377 new structures coming into the PDB archive using the web-based, global wwPDB OneDep software system for deposition, validation, and biocuration. Also, in 2019, RCSB PDB, PDBe, and PDBj jointly enabled download of ~800 million PDB structure data files by millions of users from around the world.Today, wwPDB partners are confronting significant software engineering challenges, resulting from(i) the relentless growth in the number and size/complexity of newly deposited MX and 3DEM structures, and (ii) the need to manage incoming data as groups of related structures (or investigations) coming from serial femtosecond X-ray crystallography (SFX) using X-ray Free Electron Lasers (XFEL) and 3DEM.

美国 RCSB 蛋白质数据库/欧洲蛋白质数据库合作项目的愿景是改善蛋白质数据库中存储的三维 (3D) 大分子结构信息的数据沉积、交付和管理。这项工作将使自然科学、物理科学和工程科学领域的研究人员、教育工作者及其学生受益。“形式（即形状/3D 结构）决定生物学中的功能”——沃森和克里克出版的 DNA 双螺旋结构首次揭示了这一点。自这一具有里程碑意义的发现以来，由生物学家、物理学家、化学家和工程师组成的跨学科协作团队已经生成了约 160,000 个通过实验确定的蛋白质和核酸 3D 结构，这些结构集中存储在称为蛋白质数据库 (PDB) 的公共数据资源中。 PDB 成立于 1971 年，是生物学领域第一个开放获取的数字数据资源，现已发展了 20,000 多倍，成为全球唯一的档案库，其中包含丰富注释的蛋白质、DNA 和 RNA 3D 结构。这一公共领域的 3D 结构数据资源对基础生物学、生物医学、生物技术和生物能源产生了巨大影响，它能够实现对天然存在和工程生物分子的原子级理解，并促进 2010 年至 2016 年间美国 (US) 食品和药物管理局批准的近 90% 新药的发现。如今，新的 PDB 结构来自高分子晶体学 (MX)、核磁共振波谱 (NMR)、单粒子冷冻电子显微镜 (3DEM) 和微晶电子衍射 (microED)。 X 射线自由电子激光器和新的结构测定综合方法正在加速生物医学研究，在原子水平上深入了解更加复杂的生物系统。冷冻电子断层扫描甚至可以研究冷冻细胞内“陷入困境”的大分子机器。自 2003 年以来，全球蛋白质数据库 (wwPDB、wwpdb.org) 合作伙伴根据公平-准确-保密-透明的 FACT 原则和公平原则将 PDB 核心档案（以下简称 PDB 档案）作为全球公共物品进行管理 可查找性-可访问性-互操作性-可重用性原则。 wwPDB 包括美国（结构生物信息学蛋白质数据库研究合作实验室，RCSB PDB）、欧洲（欧洲蛋白质数据库，PDBe）和亚洲（日本蛋白质数据库，PDBj）的本地资助合作伙伴，以及专业 NMR 资源（BioMagResBank，BMRB）。 wwPDB 还可以在美国、欧洲和亚洲之间公平分担 PDB 数据归档和管理成本。 2019 年，RCSB PDB、PDBe 和 PDBj 使用基于网络的全球 wwPDB OneDep 软件系统联合处理了 13,377 个进入 PDB 档案的新结构，用于沉积、验证和生物管理。此外，2019 年，RCSB PDB、PDBe 和 PDBj 联合支持全球数百万用户下载约 8 亿个 PDB 结构数据文件。如今，wwPDB 合作伙伴面临着重大的软件工程挑战，原因是 (i) 新沉积的 MX 和 3DEM 结构的数量和大小/复杂性不断增长，以及 (ii) 将传入数据作为组进行管理的需要 使用 X 射线自由电子激光器 (XFEL) 和 3DEM 进行系列飞秒 X 射线晶体学 (SFX) 的相关结构（或研究）。

项目成果

Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data.

• DOI: 10.1038/s41597-023-02101-6
• 发表时间: 2023-04-12
• 期刊: SCIENTIFIC DATA
• 影响因子: 9.8
• 作者: Choudhary, Preeti;Anyango, Stephen;Berrisford, John;Tolchard, James;Varadi, Mihaly;Velankar, Sameer
• 通讯作者: Velankar, Sameer

PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education.

• DOI: 10.1002/pro.4439
• 发表时间: 2022-10
• 期刊: PROTEIN SCIENCE
• 影响因子: 8
• 作者: Varadi, Mihaly;Anyango, Stephen;Appasamy, Sri Devan;Armstrong, David;Bage, Marcus;Berrisford, John;Choudhary, Preeti;Bertoni, Damian;Deshpande, Mandar;Leines, Grisell Diaz;Ellaway, Joseph;Evans, Genevieve;Gaborova, Romana;Gupta, Deepti;Gutmanas, Aleksandras;Harrus, Deborah;Kleywegt, Gerard J.;Bueno, Weslley Morellato;Nadzirin, Nurul;Nair, Sreenath;Pravda, Lukas;Afonso, Marcelo Querino Lima;Sehnal, David;Tanweer, Ahsan;Tolchard, James;Abrams, Charlotte;Dunlop, Roisin;Velankar, Sameer
• 通讯作者: Velankar, Sameer

Assessing PDB macromolecular crystal structure confidence at the individual amino acid residue level.

• DOI: 10.1016/j.str.2022.08.004
• 发表时间: 2022-10-06
• 期刊: STRUCTURE
• 影响因子: 5.7
• 作者: Shao, Chenghua;Bittrich, Sebastian;Wang, Sijian;Burley, Stephen K.
• 通讯作者: Burley, Stephen K.

EMDB-the Electron Microscopy Data Bank.

• DOI: 10.1093/nar/gkad1019
• 发表时间: 2024-01-05
• 期刊: NUCLEIC ACIDS RESEARCH
• 影响因子: 14.9
• 作者: Turner, Jack;Abbott, Sanja;Fonseca, Neli;Carrijo, Lucas;Duraisamy, Amudha Kumari;Salih, Osman;Wang, Zhe;Kleywegt, Gerard J.;Morris, Kyle L.;Patwardhan, Ardan;Burley, Stephen K.;Crichlow, Gregg;Feng, Zukang;Flatt, Justin W.;Ghosh, Sutapa;Hudson, Brian P.;Lawson, Catherine L.;Liang, Yuhe;Peisach, Ezra;Persikova, Irina;Sekharan, Monica;Shao, Chenghua;Young, Jasmine;Velankar, Sameer;Armstrong, David;Bage, Marcus;Bueno, Wesley Morellato;Evans, Genevieve;Gaborova, Romana;Ganguly, Sudakshina;Gupta, Deepti;Harrus, Deborah;Tanweer, Ahsan;Bansal, Manju;Rangannan, Vetriselvi;Kurisu, Genji;Cho, Hasumi;Ikegawa, Yasuyo;Kengaku, Yumiko;Kim, Ju Yaen;Niwa, Satomi;Sato, Junko;Takuwa, Ayako;Yu, Jian;Hoch, Jeffrey C.;Baskaran, Kumaran;Xu, Wenqing;Zhang, Weizhe;Ma, Xiaodan
• 通讯作者: Ma, Xiaodan

PDB NextGen Archive: Centralising Access to Integrated Annotations and Enriched Structural Information by the Worldwide Protein Data Bank

PDB NextGen Archive：通过全球蛋白质数据库集中访问集成注释和丰富的结构信息

• DOI: 10.1101/2023.10.24.563739
• 发表时间: 2023
• 作者: Choudhary P