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.

这个美国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存储，交付和管理。这项工作将有利于研究人员，教育工作者和他们的学生跨越自然，物理和工程科学。“形式（意思是形状/3D结构）决定了生物学的功能”--最早是在沃森和克里克发表的DNA双螺旋结构中发现的。自从他们的里程碑式发现以来，生物学家，物理学家，化学家和工程师的跨学科合作团队已经生成了约160，000个实验确定的蛋白质和核酸的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，是生物学中第一个开放获取的数字数据资源，现已发展超过20，000倍，成为单一的全球档案馆，其中包含蛋白质、DNA和RNA的丰富注释的3D结构。这个公共领域的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的影响，它使人们能够从原子水平上理解天然存在的和工程化的生物分子，并促进了2010-2016年间美国食品和药物管理局批准的近90%的新药的发现。如今，新的PDB结构来自大分子晶体学（MX）、核磁共振谱（NMR）、单粒子低温电子显微镜（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复杂的生物系统。自2003年以来，全球蛋白质数据库（wwPDB，wwpdb.org）合作伙伴关系根据公平-准确-保密-透明的FACT原则和可查找-可访问-互操作性-可重用的FAIR原则，将PDB核心档案（以下简称PDB档案）作为全球公共产品进行管理。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档案库的新结构，用于沉积，验证和生物定位。此外，在2019年，RCSB PDB、PDBe和PDBj共同实现了来自世界各地数百万用户的约8亿PDB结构数据文件的下载。今天，wwPDB合作伙伴面临着重大的软件工程挑战，这是由于（i）新沉积的MX和3DEM结构的数量和大小/复杂性的持续增长，和（ii）需要管理传入的数据，作为相关结构（或调查）的组来自串行飞秒X射线晶体学（SFX）使用X射线自由电子激光（XFEL）和3DEM。

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