Evidence map›Paper›PMID 36738985›Full record

ArticleJournal of molecular biology2023

RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances.

Sebastian Bittrich, Charmi Bhikadiya, Chunxiao Bi, Henry Chao, Jose M Duarte, Shuchismita Dutta, Maryam Fayazi, Jeremy Henry, Igor Khokhriakov, Robert Lowe and 7 more

Open access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of molecular biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.

0numbers the graph read from it
0cells of the map it votes in
40citing papers in PubMed
10.5field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

40 citing papers in PubMed, 68 citations in OpenAlex.

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  15. Computational Study of Enzyme Inhibition.Methods in molecular biology (Clifton, N.J.) · 2026
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

17 authors at 2 institutions in 1 country.

Sebastian BittrichResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA. Electronic address: sebastian.bittrich@rcsb.org.
Charmi BhikadiyaResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA.
Chunxiao BiResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA.
Henry ChaoResearch 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.
Jose M DuarteResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA.
Shuchismita DuttaResearch 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.
Maryam FayaziResearch 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.
Jeremy HenryResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA.
Igor KhokhriakovResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA.
Robert 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, USA.
Dennis W PiehlResearch 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.
Joan SeguraResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA.
Brinda VallatResearch 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.
Maria VoigtResearch 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.
John D 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.
Stephen K BurleyResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA; Research 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; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Yana RoseResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA.
Rutgers, The State University of New Jersey · USSan Diego Supercomputer Center · US

Funding

PDB MANAGEMENT BY THE RESEARCH COLLABORATORY FOR STRUCTURAL BIOINFORMATICSR01GM133198 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI BURLEY, STEPHEN K · 2019 to 2023
$19.3M
NIGMS NIH HHS R01 GM133198
6 · The paper itself

Abstract

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) provides open access to experimentally-determined three-dimensional (3D) structures of biomolecules. The RCSB PDB RCSB.org research-focused web portal is used annually by many millions of users around the world. They access biostructure information, run complex queries utilizing various search services (e.g., full-text, structural and chemical attribute, chemical, sequence, and structure similarity searches), and visualize macromolecules in 3D, all at no charge and with no limitations on data usage. Notwithstanding more than 24,000-fold growth of the PDB over the past five decades, experimentally-determined structures are only available for a small subset of the millions of proteins of known sequence. Recently developed machine learning software tools can predict 3D structures of proteins at accuracies comparable to lower-resolution experimental methods. The RCSB PDB now provides access to ∼1,000,000 Computed Structure Models (CSMs) of proteins coming from AlphaFold DB and the ModelArchive alongside ∼200,000 experimentally-determined PDB structures. Both CSMs and PDB structures are available on RCSB.org and via well-established RCSB PDB Data, Search, and 1D-Coordinates application programming interfaces (APIs). Simultaneous delivery of PDB data and CSMs provides users with access to complementary structural information across the human proteome and those of model organisms and selected pathogens. API enhancements are backwards-compatible and programmatic users can "opt in" to access CSMs with minimal effort. Herein, we describe modifications to RCSB PDB cyberinfrastructure required to support sixfold scaling of 3D biostructure data delivery and lay the groundwork for scaling to accommodate hundreds of millions of CSMs.

Indexed as

Computational BiologyDatabases, ProteinHumansProtein ConformationProteomeSoftwareProteomecomputer architecturedatabasesFAIR principlesprotein structure predictionstructural biology

Identifiers

PMID36738985
PMCPMC11514064
OpenAlexW4318978985

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.