{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:35Z","timestamp":1772138075614,"version":"3.50.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2025,7,10]],"date-time":"2025-07-10T00:00:00Z","timestamp":1752105600000},"content-version":"vor","delay-in-days":9,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000921","name":"European Cooperation in Science and Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000921","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Center for Gene Therapy and Drugs based on RNA Technology","award":["CN00000041"],"award-info":[{"award-number":["CN00000041"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>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\u2013function 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 \u201cperfect\u201d and often contain insertions and deletions. Existing tools for predicting structural symmetry work well on simple cases but often fail for most natural proteins.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>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\u2013Bryan angles. GeomeTRe\u2019s 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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>GeomeTRe is available as a Python package; source code and documentation can be found at https:\/\/github.com\/BioComputingUP\/GeomeTRe.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf395","type":"journal-article","created":{"date-parts":[[2025,7,10]],"date-time":"2025-07-10T14:23:26Z","timestamp":1752157406000},"source":"Crossref","is-referenced-by-count":0,"title":["GeomeTRe: accurate calculation of geometrical descriptors of tandem repeat proteins"],"prefix":"10.1093","volume":"41","author":[{"given":"Zarifa","family":"Osmanli","sequence":"first","affiliation":[{"name":"Department of Biomedical Sciences, University of Padova , Padova, 35121,","place":["Italy"]}]},{"given":"Elisa","family":"Ferrero","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, University of Padova , Padova, 35121,","place":["Italy"]},{"name":"Galileian School of Higher Education, University of Padova , Padova, 35132,","place":["Italy"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0362-8218","authenticated-orcid":false,"given":"Alexander Miguel","family":"Monzon","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, University of Padova , Padova, 35121,","place":["Italy"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4525-7793","authenticated-orcid":false,"given":"Silvio C E","family":"Tosatto","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, University of Padova , Padova, 35121,","place":["Italy"]},{"name":"Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR-IBIOM) , Bari, 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