Journal Article

FlatProt: 2D visualization eases protein structure comparison

Rost, Burkhard, Olenyi, Tobias, Senoner, Tobias, Koludarov, Ivan, Carl, Constantin

2025

Overview

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 ).

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Algorithms / Annotations / Bioinformatics / Bioinformatics tools / Biomedical and Life Sciences / Case studies / Computational Biology - methods / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Computer Graphics / Computer programs / Databases, Protein / Humans / Image processing / Inspection / Life Sciences / Methods / Microarrays / Models, Molecular / Molecular biology / Protein Conformation / Protein structure / Protein visualization / Proteins / Proteins - chemistry / Proteomes / Sequence comparison / Software / Structure / Three dimensional models / User-Computer Interface / Visualization / Visualization (Computers)