FlatProt: 2D visualization eases protein structure comparison
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Background
Understanding and comparing three-dimensional (3D) structures of proteins can advance bioinformatics, molecular biology, and drug discovery. While 3D models offer detailed insights, comparing multiple structures simultaneously remains challenging, especially on two-dimensional (2D) displays. Existing 2D visualization tools lack standardized approaches for comparing protein families, limiting their utility in structural analysis.
Results
We introduce FlatProt, designed to enhance protein structure comparison through standardized 2D visualization. Combining rotation algorithms with Foldseek structure alignments enables consistent family-wide visualization and comparison. FlatProt efficiently processes proteins of various sizes (2-34,350 residues), demonstrating its effectiveness through applications on Three-Finger Toxins (3FT), Kallikreins (KLK), and multi-domain proteins.
Conclusion
FlatProt provides clear, consistent, user-friendly visualizations that efficiently compare protein structures within and across families. It advances protein structure analysis by enabling standardized structural comparisons at scale.
Availability
GitHub ( https://github.com/t03i/FlatProt ); Zenodo ( https://doi.org/10.5281/zenodo.15264810 ).
