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

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• The tool highlights discrepancies that could arise from outdated structure files.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.