# GeomeTRe: accurate calculation of geometrical descriptors of tandem repeat proteins

## TL;DR

GeomeTRe is a new tool that accurately calculates geometric features of tandem repeat proteins, helping to better understand their structure and function.

## Contribution

GeomeTRe introduces a novel algorithm for calculating precise geometric descriptors of tandem repeat proteins with known repeat units.

## Key findings

- GeomeTRe calculates curvature, twist, and pitch by simulating the movement of consecutive repeat units.
- The algorithm identifies rotational axes and Tait–Bryan angles for improved STRP classification.
- GeomeTRe is efficient and suitable for large-scale protein structure datasets when repeat information is available.

## Abstract

Structured tandem repeat proteins (STRPs) are characterized by preserved structural motifs arranged in a modular way. The structural and functional diversity of STRPs makes them particularly important for studying evolution and novel structure–function relationships, and ultimately for designing new synthetic proteins with specific functions. One crucial aspect of their classification is the estimation of geometrical parameters, which can provide better insight into their properties and the relationship between the spatial arrangement of repeated units and protein function. Calculating geometric descriptors for STRPs is challenging because naturally occurring repeats are not “perfect” and often contain insertions and deletions. Existing tools for predicting structural symmetry work well on simple cases but often fail for most natural proteins.

Here, we present GeomeTRe, an algorithm that calculates geometrical descriptors such as curvature (yaw), twist (roll), and pitch for a protein structure with known repeat unit positions. The algorithm simulates the movement of consecutive units, identifies rotational axes, and calculates the corresponding Tait–Bryan angles. GeomeTRe’s parameters can enhance STRP annotation and classification by identifying variations in geometric arrangements among different functional groups. The package is fast and suitable for processing large protein structure datasets when repeat region information (e.g. from RepeatsDB) is available.

GeomeTRe is available as a Python package; source code and documentation can be found at https://github.com/BioComputingUP/GeomeTRe.