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Elisa Ferrero

dblp:426/2003 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2025
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 2 heaviest of 2, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology
structural bioinformatics
0.912025
GeomeTRe: accurate calculation of geometrical descriptors of tandem repeat proteins · Bioinform. 2025
Bioinformatics and computational biology › structural bioinformatics
protein structure classification
0.312025
GeomeTRe: accurate calculation of geometrical descriptors of tandem repeat proteins · Bioinform. 2025

Methods — techniques the papers use, named apart from their topics

tait-bryan angle computation · 0.9rotational axis identification · 0.9
YearPublicationVenuePosition
2025 GeomeTRe: accurate calculation of geometrical descriptors of tandem repeat proteins
abstract
MOTIVATION: 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. RESULTS: 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. AVAILABILITY AND IMPLEMENTATION: GeomeTRe is available as a Python package; source code and documentation can be found at https://github.com/BioComputingUP/GeomeTRe.
Zarifa Osmanli, Elisa Ferrero, Alexander Miguel Monzon, Silvio C. E. Tosatto, Damiano Piovesan
Bioinform.2