Duplicate entries in the Protein Data Bank: how to detect and handle them

A global analysis of protein crystal structures in the Protein Data Bank (PDB) using a newly developed computational approach reveals many pairs with (nearly) identical main-chain coordinates. Such cases are identified and analyzed, showing that duplication is possible since the PDB does not currently have tools or mechanisms that would detect potentially duplicate submissions. Some duplicated entries represent modeling efforts of ligand binding that masquerade as experimentally determined structures. We propose that duplicate entries should either be obsoleted by the PDB or, as a minimum, marked with a clear `CAVEAT' record that would alert potential users to the presence of such problems. We also suggest that using a tool for verifying the uniqueness of the deposited structure, such as that presented in this work, should become part of the routine validation procedure for new depositions.

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Publication Details

Journal
Acta Crystallographica Section D Structural Biology
Published
2025-03-08
DOI
https://doi.org/10.1107/s2059798325001883
Citations
7
Primary Topic
Enzyme Structure and Function
Type
article
Field-Weighted Citation Impact
3.62

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article

Duplicate entries in the Protein Data Bank: how to detect and handle them

W. Minor, Olga Anosova, Zbigniew Dauter, Alexander Wlodawer et al.
7 citations
Acta Crystallographica Section D Structural Biology
Enzyme Structure and Function
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article

Duplicate entries in the Protein Data Bank: how to detect and handle them

W. Minor, Olga Anosova, Zbigniew Dauter, Alexander Wlodawer, Mariusz Jaskólski, Vitaliy A. Kurlin, Paweł Rubach, William Jeffcott, Ziqiu Jiang
article en
7 citations

Abstract

A global analysis of protein crystal structures in the Protein Data Bank (PDB) using a newly developed computational approach reveals many pairs with (nearly) identical main-chain coordinates. Such cases are identified and analyzed, showing that duplication is possible since the PDB does not currently have tools or mechanisms that would detect potentially duplicate submissions. Some duplicated entries represent modeling efforts of ligand binding that masquerade as experimentally determined structures. We propose that duplicate entries should either be obsoleted by the PDB or, as a minimum, marked with a clear `CAVEAT' record that would alert potential users to the presence of such problems. We also suggest that using a tool for verifying the uniqueness of the deposited structure, such as that presented in this work, should become part of the routine validation procedure for new depositions.

Acta Crystallographica Section D Structural BiologyVol. 81(4)
University of Liverpool (GB), SGH Warsaw School of Economics (PL), National Cancer Institute (US), Center for Cancer Research (US), Institute of Bioorganic Chemistry, Polish Academy of Sciences (PL), Imperial College London (GB), University of Virginia (US), Adam Mickiewicz University in Poznań (PL)
Royal Society, Engineering and Physical Sciences Research Council, National Cancer Institute, EPSRC Centre for Doctoral Training in Medical Imaging
Partnerships for the goals
Openalex Percentile: Top 7%
Enzyme Structure and Function
3.62
DOIOpen Access PDFOpenAlex
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