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RCSB Protein Data Bank: Architectural advances towards integrated searching and efficient access to macromolecular structure data from the PDB archive
Journal of Molecular Biology ( IF 5.6 ) Pub Date : 2020-11-10 , DOI: 10.1016/j.jmb.2020.11.003
Yana Rose 1 , Jose M Duarte 1 , Robert Lowe 2 , Joan Segura 1 , Chunxiao Bi 1 , Charmi Bhikadiya 2 , Li Chen 2 , Alexander S Rose 1 , Sebastian Bittrich 1 , Stephen K Burley 3 , John D Westbrook 4
Affiliation  

The US Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) serves many millions of unique users worldwide by delivering experimentally-determined 3D structures of biomolecules integrated with >40 external data resources via RCSB.org, application programming interfaces (APIs), and FTP downloads. Herein, we present the architectural redesign of RCSB PDB data delivery services that build on existing PDBx/mmCIF data schemas. New data access APIs (data.rcsb.org) enable efficient delivery of all PDB archive data. A novel GraphQL-based API provides flexible, declarative data retrieval along with a simple-to-use REST API. A powerful new search system (search.rcsb.org) seamlessly integrates heterogeneous types of searches across the PDB archive. Searches may combine text attributes, protein or nucleic acid sequences, small-molecule chemical descriptors, 3D macromolecular shapes, and sequence motifs. The new RCSB.org architecture adheres to the FAIR Principles, empowering users to address a wide array of research problems in fundamental biology, biomedicine, biotechnology, bioengineering, and bioenergy.



中文翻译:

RCSB 蛋白质数据库:在集成搜索和有效访问 PDB 档案中的大分子结构数据方面的架构进展

美国结构生物信息学蛋白质数据库研究合作实验室 (RCSB PDB) 通过提供实验确定的生物分子 3D 结构并通过RCSB.org、应用程序编程接口 (API) 和超过 40 个外部数据资源集成,为全球数百万独特用户提供服务。 FTP 下载。在这里,我们展示了基于现有 PDBx/mmCIF 数据模式的 RCSB PDB 数据交付服务的架构重新设计。新的数据访问 API ( data.rcsb.org ) 可以有效地交付所有 PDB 归档数据。一种新颖的基于 GraphQL 的 API 提供了灵活的声明式数据检索以及简单易用的 REST API。一个强大的新搜索系统(search.rcsb.org) 无缝集成跨 PDB 存档的异构类型的搜索。搜索可以结合文本属性、蛋白质或核酸序列、小分子化学描述符、3D 大分子形状和序列基序。新的 RCSB.org 架构遵循 FAIR 原则,使用户能够解决基础生物学、生物医学、生物技术、生物工程和生物能源领域的广泛研究问题。

更新日期:2020-11-12
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