ArticleActa crystallographica. Section D, Structural biology2025
Duplicate entries in the Protein Data Bank: how to detect and handle them.
Article in Acta crystallographica. Section D, Structural biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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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.
The trial behind it
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Who cites it
5 citing papers in PubMed.
- Scotty: lattice coincidences in the Protein Data Bank.Acta crystallographica. Section D, Structural biology · 2026Article
- Stereochemical aspects of the nucleophilic attack in different classes of L-asparaginases.IUCrJ · 2026Review
- How to mitigate the caveat emptor burden of human and machine users of the Protein Data Bank.Acta crystallographica. Section D, Structural biology · 2026Article
- A Critical Look at the Crystal Structures of cAMP-Dependent Protein Kinases.Kinases and phosphatases · 2025Article
- Geographic-style maps with a local novelty distance help navigate in the materials space.Scientific reports · 2025Article
Corrections and comments
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Authors and funding
9 authors.
Funding
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.
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Registered trials
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.