Статья

RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive

Yana RoseResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USAJosé M. DuarteResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USARobert LoweResearch Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USAJoan SeguraResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USAChunxiao BiResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USACharmi BhikadiyaResearch Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USALi ChenResearch Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USAAlexander RoseResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USASebastian BittrichResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USAS.K. BurleyResearch Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USAJohn WestbrookResearch Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA. Electronic address: [email protected]

2020en

ABI

Аннотация

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.

Перевод пока недоступен

Идентификаторы

DOI: 10.1016/j.jmb.2020.11.003

Цитирования и источники

Цитирований: 5Использованных источников: 0

Показатели — AkademScholar