Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank

Stephen K. Burley, Rusham Bhatt, Charmi Bhikadiya, Chunxiao Bi, Alison Biester, Pratyoy Biswas, Sebastian Bittrich, Santiago Blaumann, Ronald Brown, Henry Chao, Vivek Reddy Chithari, Paul A. Craig, Gregg V. Crichlow, Jose M. Duarte, Shuchismita Dutta, Zukang Feng, Justin W. Flatt, Sutapa Ghosh, David S. Goodsell, Rachel Kramer GreenVladimir Guranovic, Jeremy Henry, Brian P. Hudson, Michael Joy, Jason T. Kaelber, Igor Khokhriakov, Jhih Siang Lai, Catherine L. Lawson, Yuhe Liang, Douglas Myers-Turnbull, Ezra Peisach, Irina Persikova, Dennis W. Piehl, Aditya Pingale, Yana Rose, Jared Sagendorf, Andrej Sali, Joan Segura, Monica Sekharan, Chenghua Shao, James Smith, Michael Trumbull, Brinda Vallat, Maria Voigt, Ben Webb, Shamara Whetstone, Amy Wu-Wu, Tongji Xing, Jasmine Y. Young, Arthur Zalevsky, Christine Zardecki

Research output: Contribution to journalArticlepeer-review

19 Scopus citations

Abstract

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.org research-focused web portal. We report substantial additions to the tools and visualization features available at RCSB.org, which now delivers more than 227000 experimentally determined atomic-level three-dimensional (3D) biostructures stored in the global PDB archive alongside more than 1 million Computed Structure Models (CSMs) of proteins (including models for human, model organisms, select human pathogens, crop plants and organisms important for addressing climate change). In addition to providing support for 3D structure motif searches with user-provided coordinates, new features highlighted herein include query results organized by redundancy-reduced Groups and summary pages that facilitate exploration of groups of similar proteins. Newly released programmatic tools are also described, as are enhanced training opportunities.

Original languageEnglish (US)
Pages (from-to)D564-D574
JournalNucleic acids research
Volume53
Issue numberD1
DOIs
StatePublished - Jan 6 2025

All Science Journal Classification (ASJC) codes

  • Genetics

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