FlatProt: 2D visualization eases protein structure comparison
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Abstract
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 pipelined inspection of large protein sets, limiting their utility in large-scale pre-filtering. Results: We introduce FlatProt, a tool designed to complement 3D viewers by enabling standardized 2D visualization of individual protein structures or large sets thereof. By including Foldseek-based family rotation alignment or an inertia-based fallback, FlatProt creates consistent and scalable visual representations for user-defined protein structures. It supports domain-aware decomposition, family-level overlays, and lightweight visual abstraction of secondary structures. FlatProt processes proteins efficiently, as showcased on a subset of the human-proteome. Conclusion: FlatProt provides clear, consistent, user-friendly visualizations that support rapid, comparative inspection of protein structures at scale. By bridging the gap between interactive 3D tools and static visual summaries, it enables users to explore conserved features, detect outliers, and prioritize structures for further analysis. Availability: GitHub ( https://github.com/t03i/FlatProt ); Zenodo ( https://doi.org/10.5281/zenodo.15697296 ).
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
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- Authors
- Olenyi, T., Carl, C., Senoner, T., Koludarov, I., & Rost, B.
- Affiliations
- Technical University of Munich (DE)
- Corresponding author
- Olenyi, Tobias
- Venue
- BMC Bioinformatics
- Published
- 2025-08-13
- Volume
- 26
- Issue
- 1
- Pages
- 210-210
- ISSN
- 1471-2105 (ISSN-L)
- PMC
- PMC12344939
- OpenAlex
- W4413116753
- Cited by
- 2
- References
- 4
- Citations by year
- 2026: 2
- FWCI
- 0.60
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- BMC Bioinformatics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Technische Universität München
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Physical Sciences › Computer Science › Computer Vision and Pattern Recognition › Data Visualization and Analytics
- Keywords
- protein structure visualization, 2D visualization, protein structure comparison, Foldseek, domain decomposition, human proteome, outlier detection
- MeSH terms
- Computer Graphics, Humans, Models, Molecular, Protein Conformation, Proteins, Software, User-Computer Interface, Computational Biology, Databases, Protein
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