FlatProt: 2D visualization eases protein structure comparison
Tobias Olenyi, Constantin Carl, Tobias Senoner, Ivan Koludarov, Burkhard Rost
TL;DR
FlatProt is a new tool that creates standardized 2D visualizations of protein structures to make large-scale comparisons easier and more efficient.
Contribution
FlatProt introduces a scalable and user-friendly 2D visualization method for protein structures, enabling efficient comparison at scale.
Findings
FlatProt uses Foldseek-based alignment and inertia-based fallback to generate consistent visualizations.
The tool supports domain-aware decomposition and family-level overlays for detailed structure analysis.
It efficiently processes large protein sets, demonstrated on a subset of the human proteome.
Abstract
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. 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…
Genes, proteins, chemicals, diseases, species, mutations and cell lines named across the full text — each resolved to its canonical identifier and authoritative record.
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Taxonomy
TopicsProtein Structure and Dynamics · Enzyme Structure and Function · RNA and protein synthesis mechanisms