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3DSeqCheck: A Web-based Tool for Verifying Sequence Consistency Between a 3D Structure File and the Corresponding

Anja Conev¹, Suhail A Islam¹, Ifigenia Tsitsa¹

¹Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.

Journal of Molecular Biology

|January 1, 2026

Summary

This summary is machine-generated.

Protein structure databases like AlphaFold can become outdated compared to UniProt sequence data. A new tool, 3DSeqCheck, helps identify and correct sequence mismatches in protein structures to prevent bioinformatics errors.

Keywords:

AlphaFoldDB UniProt molecular graphics protein structure structure check

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An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

Bioinformatics
Structural Biology
Computational Biology

Background:

UniProt is a dynamic protein sequence and annotation database, frequently updated.
Protein structure databases, such as AlphaFold, may lag behind UniProt updates, leading to data discrepancies.
Nearly 3% of sequences in UniProt were revised over four years while AlphaFold remained static, highlighting potential annotation mismatches.

Purpose of the Study:

To address the lack of tools for comparing modelled protein structures with updated UniProt sequence annotations.
To introduce 3DSeqCheck, a web tool for verifying sequence integrity in protein structures against current UniProt entries.

Main Methods:

Development of 3DSeqCheck, a lightweight web tool.
Implementation of sequence comparison between protein structures (modelled and experimental) and the latest UniProt entries.
Provision of an interactive visual panel for alignment and residue numbering comparison.

Main Results:

3DSeqCheck enables rapid comparison of protein structure sequences to current UniProt data.
The tool highlights discrepancies that could arise from outdated structure files.
Identified potential errors in downstream bioinformatics analyses due to sequence annotation mismatches.

Conclusions:

3DSeqCheck is a valuable resource for ensuring accuracy in bioinformatics tasks involving protein structure and sequence data.
The tool facilitates the detection of sequence-structure mismatches in both modelled and experimental protein structures.
Regular checking with 3DSeqCheck can improve the reliability of analyses relying on integrated protein sequence and structure information.