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RCSB 蛋白质数据库:用新工具庆祝 PDB 成立 50 周年,帮助理解和可视化 3D 生物大分子。

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D.

机构信息

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

Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.

出版信息

Protein Sci. 2022 Jan;31(1):187-208. doi: 10.1002/pro.4213. Epub 2021 Nov 6.

Abstract

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB-designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three-dimensional (3D) macromolecular structure data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) from all inhabited continents. RCSB PDB makes PDB data available from its research-focused RCSB.org web portal at no charge and without usage restrictions to millions of PDB data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and education PDB101.RCSB.org web portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past year via the RCSB.org web portal.

摘要

美国国家科学基金会、美国国立卫生研究院和美国能源部共同资助的研究协作结构生物信息学蛋白质数据库(RCSB PDB)自 1999 年以来一直为全球结构生物学家和蛋白质数据库(PDB)数据使用者提供服务。RCSB PDB 作为全球蛋白质数据库(wwPDB)合作组织的创始成员之一,是全球 PDB 档案库的美国数据中心,该档案库保存生物分子结构数据。RCSB PDB 还负责 PDB 数据的安全性,作为 wwPDB 指定的档案管理员。每年,RCSB PDB 为数以万计的来自各大洲的三维(3D)大分子结构数据提交者(使用大分子晶体学、核磁共振波谱学、电子显微镜和微电子衍射)提供服务。RCSB PDB 通过其以研究为重点的 RCSB.org 门户网站免费提供 PDB 数据,且没有使用限制,数以百万计的全球 PDB 数据使用者可在全球任何国家和地区使用。此外,RCSB PDB 还运营着一个外展和教育 PDB101.RCSB.org 门户网站,该网站在 2020 年被 80 多万教育工作者、学生和公众使用。本特邀工具专刊介绍了(i)随着新的实验方法生成越来越大、越来越复杂的生物分子结构,档案库如何发展和演变;(ii)数据标准和数据修复在有效管理档案库以及与 50 多个外部数据资源轻松集成方面的重要性;以及(iii)在过去一年中通过 RCSB.org 门户网站提供的 3D 结构分析和可视化的新工具和功能。

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