STRPsearch: fast detection of structured tandem repeat proteins Article Swipe
Soroush Mozaffari
,
Paula Nazarena Arrías
,
Damiano Clementel
,
Damiano Piovesan
,
Carlo Ferrari
,
Silvio C. E. Tosatto
,
Alexander Miguel Monzón
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1093/bioinformatics/btae690
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1093/bioinformatics/btae690
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. Availability and implementation STRPsearch is coded in Python. All scripts and associated documentation are available from: https://github.com/BioComputingUP/STRPsearch.
Related Topics
Concepts
Python (programming language)
Computer science
Scripting language
Tandem repeat
Scalability
Documentation
Computational biology
Proteome
Structural bioinformatics
Identification (biology)
Data mining
Artificial intelligence
Protein structure
Programming language
Bioinformatics
Biology
Database
Genetics
Genome
Gene
Biochemistry
Botany
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/bioinformatics/btae690
- OA Status
- gold
- Cited By
- 2
- References
- 23
- Related Works
- 10
- OpenAlex ID
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All OpenAlex metadata
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https://openalex.org/W4404509638Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1093/bioinformatics/btae690Digital Object Identifier
- Title
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STRPsearch: fast detection of structured tandem repeat proteinsWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2024Year of publication
- Publication date
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2024-11-14Full publication date if available
- Authors
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Soroush Mozaffari, Paula Nazarena Arrías, Damiano Clementel, Damiano Piovesan, Carlo Ferrari, Silvio C. E. Tosatto, Alexander Miguel MonzónList of authors in order
- Landing page
-
https://doi.org/10.1093/bioinformatics/btae690Publisher landing page
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://doi.org/10.1093/bioinformatics/btae690Direct OA link when available
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Python (programming language), Computer science, Scripting language, Tandem repeat, Scalability, Documentation, Computational biology, Proteome, Structural bioinformatics, Identification (biology), Data mining, Artificial intelligence, Protein structure, Programming language, Bioinformatics, Biology, Database, Genetics, Genome, Gene, Biochemistry, BotanyTop concepts (fields/topics) attached by OpenAlex
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2Total citation count in OpenAlex
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2025: 1, 2024: 1Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.experimental | 205 |
| abstract_inverted_index.arrangements, | 28 |
| abstract_inverted_index.characterized | 13 |
| abstract_inverted_index.comprehensive | 225 |
| abstract_inverted_index.documentation | 245 |
| abstract_inverted_index.impracticable | 120 |
| abstract_inverted_index.conformational | 151 |
| abstract_inverted_index.implementation | 235 |
| abstract_inverted_index.classification, | 137 |
| abstract_inverted_index.identification, | 136 |
| abstract_inverted_index.state-of-the-art | 85 |
| abstract_inverted_index.https://github.com/BioComputingUP/STRPsearch. | 249 |
| cited_by_percentile_year.max | 95 |
| cited_by_percentile_year.min | 90 |
| countries_distinct_count | 2 |
| institutions_distinct_count | 7 |
| citation_normalized_percentile.value | 0.7137146 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |