3DSeqCheck: a web-based tool for verifying sequence consistency between a 3D structure file and the corresponding UniProt entry
File(s)
Published version
Author(s)
Conev, Anja
Islam, Suhail A
Tsitsa, Ifigenia
David, Alessia
Sternberg, Michael JE
Type
Journal Article
Abstract
UniProt is a central repository of protein sequences and annotations, with entries being updated several times a year as new sequencing evidence is collected. By contrast, protein structure resources often evolve at a different pace. The AlphaFold database remained unchanged for four years, until September 2025, during which time nearly 3% of the associated sequences underwent revisions in UniProt. In a range of bioinformatics tasks, protein structure data is paired with sequence annotations from UniProt. Mapping annotations to outdated structure files can lead to errors in downstream analysis. While this concern has been addressed for experimental structures, efforts for the modeled structures are lacking. 3DSeqCheck is a lightweight web tool that enables quick comparison of the sequence of modeled and experimental structures to the latest UniProt entries. 3DSeqCheck provides an interactive visual panel of the alignment and the comparison of the residue numbering and can be accessed freely at: https://missense3d.bc.ic.ac.uk/3dseqcheck and https://github.ic.ac.uk/ImperialCollegeLondon/check3Dseq.
Date Issued
2026-09-15
Date Acceptance
2025-12-26
Citation
Journal of Molecular Biology, 2026, 438 (18)
ISSN
0022-2836
Publisher
Elsevier
Journal / Book Title
Journal of Molecular Biology
Volume
438
Issue
18
Copyright Statement
© 2025 The Author(s). Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/ licenses/by/4.0/).
License URL
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/41478603
PII: S0022-2836(25)00686-2
Subjects
AlphaFoldDB
UniProt
molecular graphics
protein structure
structure check
Publication Status
Published
Coverage Spatial
Netherlands
Article Number
169620
Date Publish Online
2025-12-30