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蛋白质数据库档案。

The Protein Data Bank Archive.

机构信息

Protein Data Bank in Europe, European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.

Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.

出版信息

Methods Mol Biol. 2021;2305:3-21. doi: 10.1007/978-1-0716-1406-8_1.

Abstract

Protein Data Bank is the single worldwide archive of experimentally determined macromolecular structure data. Established in 1971 as the first open access data resource in biology, the PDB archive is managed by the worldwide Protein Data Bank (wwPDB) consortium which has four partners-the RCSB Protein Data Bank (RCSB PDB; rcsb.org), the Protein Data Bank Japan (PDBj; pdbj.org), the Protein Data Bank in Europe (PDBe; pdbe.org), and BioMagResBank (BMRB; www.bmrb.wisc.edu ). The PDB archive currently includes ~175,000 entries. The wwPDB has established a number of task forces and working groups that bring together experts form the community who provide recommendations on improving data standards and data validation for improving data quality and integrity. The wwPDB members continue to develop the joint deposition, biocuration, and validation system (OneDep) to improve data quality and accommodate new data from emerging techniques such as 3DEM. Each PDB entry contains coordinate model and associated metadata for all experimentally determined atomic structures, experimental data for the traditional structure determination techniques (X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy), validation reports, and additional information on quaternary structures. The wwPDB partners are committed to following the FAIR (Findability, Accessibility, Interoperability, and Reproducibility) principles and have implemented a DOI resolution mechanism that provides access to all the relevant files for a given PDB entry. On average, >250 new entries are added to the archive every week and made available by each wwPDB partner via FTP area. The wwPDB partner sites also develop data access and analysis tools and make these available via their websites. wwPDB continues to work with experts in the community to establish a federation of archives for archiving structures determined using integrative/hybrid method where multiple experimental techniques are used.

摘要

蛋白质数据库是一个用于储存生物大分子结构数据的国际合作组织。该数据库于 1971 年成立,是生物学领域首个开放获取的数据资源。目前,该数据库由全球蛋白质数据库(wwPDB)联盟管理,该联盟由四个合作伙伴组成:美国国家生物信息中心蛋白质数据库(RCSB PDB;rcsb.org)、日本蛋白质数据库(PDBj;pdbj.org)、欧洲蛋白质数据库(PDBe;pdbe.org)和生物磁共振生物分子资源库(BMRB;www.bmrb.wisc.edu)。该数据库目前收录了约 17.5 万个条目。wwPDB 成立了多个工作组,召集了社区专家,为提高数据标准和数据验证水平提供建议,以提高数据质量和完整性。wwPDB 成员还在继续开发联合提交、生物信息学和验证系统(OneDep),以提高数据质量,适应新兴技术(如 3DEM)产生的新数据。每个 PDB 条目都包含通过实验确定的所有原子结构的坐标模型和相关元数据、传统结构测定技术(X 射线晶体学和核磁共振(NMR)光谱学)的实验数据、验证报告以及四级结构的其他信息。wwPDB 的合作伙伴致力于遵循 FAIR(可发现性、可访问性、互操作性和可重复性)原则,并实施了 DOI 解析机制,该机制可获取给定 PDB 条目的所有相关文件。平均每周有超过 250 个新条目添加到数据库中,wwPDB 的每个合作伙伴都通过 FTP 区域提供这些条目。wwPDB 的合作伙伴网站还开发了数据访问和分析工具,并通过其网站提供这些工具。wwPDB 还将继续与社区专家合作,建立一个整合/混合方法结构存档联盟,该联盟将使用多种实验技术来存档结构。

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