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Cited by 31Enzyme Structure and FunctionProtein Structure and DynamicsCrystal structures of chemical compounds

New Biological Insights from Better Structure Models

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Touw, Wouter G., Joosten, Robbie P., Vriend, Gert·2016·Journal of Molecular Biology
DOI 10.1016/j.jmb.2016.02.002
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Abstract

Structure validation is a key component of all steps in the structure determination process, from structure building, refinement, deposition, and evaluation all the way to post-deposition optimisation of structures in the Protein Data Bank (PDB) by re-refinement and re-building. Today, many aspects of protein structures are understood better than 10years ago, and combined with improved software and more computing power, the automated PDB_REDO procedure can significantly improve about 85% of all X-ray structures ever deposited in the PDB. We review structure validation, structure improvement, and a series of validation resources and facilities that give access to improved PDB files and to reports on the quality of the original and the improved structures. Post-deposition optimisation generally leads to improved protein structures and a series of examples will illustrate how that, in turn, leads to improved or even novel biological insights.

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  • About 85% of deposited protein crystal structures contain discernable errors.

    “As a result, ∼85% of deposited protein crystal structures contain discernable errors2.”

    From Determining crystal structures through crowdsourcing and coursework (2016) · cites this paper as [2]

    The Validation section describes errors found in deposited crystal structures and methods for detecting them. The Concluding remarks also say X-ray structures may contain experimental and human errors. Neither passage, nor the passages retrieved by searching for 85% and error prevalence, supports the claim that approximately 85% of deposited protein crystal structures contain discernable errors (pages unavailable in our copy). (LLM, conf=0.84)

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Cited by

Sorted by citations

Authors
Touw, W. G., Joosten, R. P., & Vriend, G.
Affiliations
  • Radboud University Medical Center (NL)
  • The Netherlands Cancer Institute (NL)
Corresponding author
Vriend, Gert
ORCID
Venue
Journal of Molecular Biology
Publisher
Elsevier BV
Published
2016-03
Volume
428
Issue
6
Pages
1375-1393
ISSN
0022-2836 (ISSN-L)
DOI
10.1016/j.jmb.2016.02.002
OpenAlex
W2269059522
Cited by
31
References
0
Citations by year
2025: 1 · 2024: 1 · 2023: 1 · 2022: 1 · 2021: 3 · 2020: 2 · 2019: 5 · 2018: 2 · 2017: 5 · 2016: 10
FWCI
0.29
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of Molecular Biology (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Radboud Repository (Radboud University) (submittedVersion)
  • Radboud Repository (Radboud University) (submittedVersion, other-oa)
Funders
  • European Commission (289350)
  • Netherlands Organization for Scientific Research
Topics
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Chemistry › Inorganic Chemistry › Crystal structures of chemical compounds
Keywords
protein structure validation, X-ray crystallography, Protein Data Bank
MeSH terms
Models, Molecular, Protein Conformation, Proteins, Crystallography, X-Ray, Computational Biology

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