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 Green; Vladimir 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

doi:10.1093/nar/gkae1091

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

Nucleic Acids Res. 2024 Nov 28:gkae1091. doi: 10.1093/nar/gkae1091. Online ahead of print.

Authors

Stephen K Burley^{1

2

3

4

5

6}, Rusham Bhatt^{1

2}, Charmi Bhikadiya⁵, Chunxiao Bi⁵, Alison Biester^{1

2}, Pratyoy Biswas^{1

2}, Sebastian Bittrich⁵, Santiago Blaumann^{1

2}, Ronald Brown^{1

2}, Henry Chao^{1

2}, Vivek Reddy Chithari^{1

2}, Paul A Craig⁷, Gregg V Crichlow^{1

2}, Jose M Duarte⁵, Shuchismita Dutta^{1

2

3}, Zukang Feng^{1

2}, Justin W Flatt^{1

2}, Sutapa Ghosh^{1

2}, David S Goodsell^{1

2

3

8}, Rachel Kramer Green¹, Vladimir Guranovic^{1

2}, Jeremy Henry⁵, Brian P Hudson^{1

2}, Michael Joy^{1

2}, Jason T Kaelber^{1

2}, Igor Khokhriakov⁵, Jhih-Siang Lai⁵, Catherine L Lawson^{1

2}, Yuhe Liang^{1

2}, Douglas Myers-Turnbull⁵, Ezra Peisach^{1

2}, Irina Persikova^{1

2}, Dennis W Piehl^{1

2}, Aditya Pingale^{1

2}, Yana Rose⁵, Jared Sagendorf⁹, Andrej Sali⁹, Joan Segura⁵, Monica Sekharan^{1

2}, Chenghua Shao^{1

2}, James Smith^{1

2}, Michael Trumbull^{1

2}, Brinda Vallat^{1

2}, Maria Voigt^{1

2}, Ben Webb⁹, Shamara Whetstone^{1

2}, Amy Wu-Wu^{1

2}, Tongji Xing^{1

2}, Jasmine Y Young^{1

2}, Arthur Zalevsky⁹, Christine Zardecki^{1

2}

Affiliations

¹ Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
² Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
³ Rutgers Cancer Institute, New Brunswick, NJ 08901, USA.
⁴ Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
⁵ Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA.
⁶ Rutgers Artificial Intelligence and Data Science (RAD) Collaboratory, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
⁷ School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, NY 14623, USA.
⁸ Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
⁹ Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California, San Francisco, CA 94158, USA.

PMID: 39607707
DOI: 10.1093/nar/gkae1091

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.

Abstract

Grants and funding