kth.sePublications KTH
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
STRPsearch: fast detection of structured tandem repeat proteins
Department of Biomedical Sciences, University of Padova, Padova 35121, Italy.
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Protein Technology. Department of Biomedical Sciences, University of Padova, Padova 35121, Italy.ORCID iD: 0000-0001-5668-768X
Department of Biomedical Sciences, University of Padova, Padova 35121, Italy.
Department of Biomedical Sciences, University of Padova, Padova 35121, Italy.
Show others and affiliations
2024 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 40, no 12, article id btae690Article in journal (Refereed) Published
Abstract [en]

Motivation: Structured Tandem Repeats Proteins (STRPs) constitute a subclass of tandem repeats characterized by repetitive structural motifs. These proteins exhibit distinct secondary structures that form repetitive tertiary arrangements, often resulting in large molecular assemblies. Despite highly variable sequences, STRPs can perform important and diverse biological functions, maintaining a consistent structure with a variable number of repeat units. With the advent of protein structure prediction methods, millions of 3D models of proteins are now publicly available. However, automatic detection of STRPs remains challenging with current state-of-the-art tools due to their lack of accuracy and long execution times, hindering their application on large datasets. In most cases, manual curation remains the most accurate method for detecting and classifying STRPs, making it impracticable to annotate millions of structures. Results: We introduce STRPsearch, a novel tool for the rapid identification, classification, and mapping of STRPs. Leveraging manually curated entries from RepeatsDB as the known conformational space of STRPs, STRPsearch uses the latest advances in structural alignment for a fast and accurate detection of repeated structural motifs in proteins, followed by an innovative approach to map units and insertions through the generation of TM-score profiles. STRPsearch is highly scalable, efficiently processing large datasets, and can be applied to both experimental structures and predicted models. In addition, it demonstrates superior performance compared to existing tools, offering researchers a reliable and comprehensive solution for STRP analysis across diverse proteomes.

Place, publisher, year, edition, pages
Oxford University Press (OUP) , 2024. Vol. 40, no 12, article id btae690
National Category
Biochemistry Molecular Biology
Identifiers
URN: urn:nbn:se:kth:diva-358172DOI: 10.1093/bioinformatics/btae690ISI: 001377102900001PubMedID: 39558588Scopus ID: 2-s2.0-85211966531OAI: oai:DiVA.org:kth-358172DiVA, id: diva2:1924799
Note

QC 20250114

Available from: 2025-01-07 Created: 2025-01-07 Last updated: 2025-02-20Bibliographically approved

Open Access in DiVA

No full text in DiVA

Other links

Publisher's full textPubMedScopus

Authority records

Arrías, Paula

Search in DiVA

By author/editor
Arrías, Paula
By organisation
Protein Technology
In the same journal
Bioinformatics
BiochemistryMolecular Biology

Search outside of DiVA

GoogleGoogle Scholar

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 52 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf