# FlatProt: 2D visualization eases protein structure comparison

## 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.

## Key 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 abstraction of secondary structures. FlatProt processes proteins efficiently, as showcased on a subset of the human-proteome.

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.

GitHub (https://github.com/t03i/FlatProt); Zenodo (https://doi.org/10.5281/zenodo.15697296).

The online version contains supplementary material available at 10.1186/s12859-025-06233-x.