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

S.K. Burley(Rutgers, The State University of New Jersey), Rusham Bhatt(Rutgers, The State University of New Jersey), Charmi Bhikadiya(San Diego Supercomputer Center), Chunxiao Bi(San Diego Supercomputer Center), Alison Biester(Rutgers, The State University of New Jersey), Pratyoy Biswas(Rutgers, The State University of New Jersey), Sebastian Bittrich(San Diego Supercomputer Center), Santiago Blaumann(Rutgers, The State University of New Jersey), Ronald Brown(Rutgers, The State University of New Jersey), Henry Chao(Rutgers, The State University of New Jersey), Vivek Reddy Chithari(Rutgers, The State University of New Jersey), P. Craig(Rochester Institute of Technology), G.V. Crichlow(Rutgers, The State University of New Jersey), José M. Duarte(San Diego Supercomputer Center), Shuchismita Dutta(Rutgers, The State University of New Jersey), Zukang Feng(Rutgers, The State University of New Jersey), Justin W. Flatt(Rutgers, The State University of New Jersey), Sutapa Ghosh(Rutgers, The State University of New Jersey), David S. Goodsell(Rutgers, The State University of New Jersey), Rachel Kramer Green(Rutgers, The State University of New Jersey), Vladimir Guranović(Rutgers, The State University of New Jersey), Jeremy Henry(San Diego Supercomputer Center), Brian P. Hudson(Rutgers, The State University of New Jersey), Mariya Joy(Rutgers, The State University of New Jersey), Jason T. Kaelber(Rutgers, The State University of New Jersey), Igor Khokhriakov(San Diego Supercomputer Center), Jhih‐Siang Lai(San Diego Supercomputer Center), Catherine L. Lawson(Rutgers, The State University of New Jersey), Yu‐He Liang(Rutgers, The State University of New Jersey), Douglas Myers-Turnbull(San Diego Supercomputer Center), Ezra Peisach(Rutgers, The State University of New Jersey), Irina Persikova(Rutgers, The State University of New Jersey), Dennis W. Piehl(Rutgers, The State University of New Jersey), Aditya Pingale(Rutgers, The State University of New Jersey), Yana Rose(San Diego Supercomputer Center), Jared M. Sagendorf(QB3), Andrej Šali(QB3), Joan Segura(San Diego Supercomputer Center), Monica Sekharan(Rutgers, The State University of New Jersey), Chenghua Shao(Rutgers, The State University of New Jersey), James M. Smith(Rutgers, The State University of New Jersey), Michael Trumbull(Rutgers, The State University of New Jersey), Brinda Vallat(Rutgers, The State University of New Jersey), Maria Voigt(Rutgers, The State University of New Jersey), Ben Webb(QB3), Shamara Whetstone(Rutgers, The State University of New Jersey), Amy Wu-Wu(Rutgers, The State University of New Jersey), Tongji Xing(Rutgers, The State University of New Jersey), Jasmine Young(Rutgers, The State University of New Jersey), Arthur O. Zalevsky(QB3), Christine Zardecki(Rutgers, The State University of New Jersey)
Nucleic Acids Research
October 28, 2024
10.1093/nar/gkae1091
Cited by 239Open Access
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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.

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