ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations
Abstract Non-coding RNA functions are largely defined by their 3D structures, which consist of recurrent building blocks, tertiary motifs. The computational motif search problem remains largely unsolved, as standard approaches are restrained by sequence, interactions, or backbone topology. We presen...
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| Format: | Article |
| Language: | English |
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BMC
2025-07-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-025-03696-2 |
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| author | Eugene F. Baulin Davyd R. Bohdan Dawid Kowalski Milena Serwatka Julia Świerczyńska Zuzanna Żyra Janusz M. Bujnicki |
| author_facet | Eugene F. Baulin Davyd R. Bohdan Dawid Kowalski Milena Serwatka Julia Świerczyńska Zuzanna Żyra Janusz M. Bujnicki |
| author_sort | Eugene F. Baulin |
| collection | DOAJ |
| description | Abstract Non-coding RNA functions are largely defined by their 3D structures, which consist of recurrent building blocks, tertiary motifs. The computational motif search problem remains largely unsolved, as standard approaches are restrained by sequence, interactions, or backbone topology. We present ARTEM 2.0, which enables automated, unrestrained searches of RNA and DNA structure databases to identify 3D motifs. We apply ARTEM for searching kink-turns, G-quadruplexes, GNRA tetraloops, and i-motifs. ARTEM outperforms existing methods and enables the discovery of novel motif variants. ARTEM opens a fundamentally new way of studying nucleic acid 3D folds and motifs and analyzing their correlations and variations. |
| format | Article |
| id | doaj-art-11eacab35c9d4733a22abd33b2a8e1e3 |
| institution | DOAJ |
| issn | 1474-760X |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj-art-11eacab35c9d4733a22abd33b2a8e1e32025-08-20T03:05:21ZengBMCGenome Biology1474-760X2025-07-0126112010.1186/s13059-025-03696-2ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutationsEugene F. Baulin0Davyd R. Bohdan1Dawid Kowalski2Milena Serwatka3Julia Świerczyńska4Zuzanna Żyra5Janusz M. Bujnicki6International Institute of Molecular and Cell Biology in WarsawInternational Institute of Molecular and Cell Biology in WarsawInternational Institute of Molecular and Cell Biology in WarsawInternational Institute of Molecular and Cell Biology in WarsawInternational Institute of Molecular and Cell Biology in WarsawInternational Institute of Molecular and Cell Biology in WarsawInternational Institute of Molecular and Cell Biology in WarsawAbstract Non-coding RNA functions are largely defined by their 3D structures, which consist of recurrent building blocks, tertiary motifs. The computational motif search problem remains largely unsolved, as standard approaches are restrained by sequence, interactions, or backbone topology. We present ARTEM 2.0, which enables automated, unrestrained searches of RNA and DNA structure databases to identify 3D motifs. We apply ARTEM for searching kink-turns, G-quadruplexes, GNRA tetraloops, and i-motifs. ARTEM outperforms existing methods and enables the discovery of novel motif variants. ARTEM opens a fundamentally new way of studying nucleic acid 3D folds and motifs and analyzing their correlations and variations.https://doi.org/10.1186/s13059-025-03696-2Kink-turnK-junctionA-minor junctionTertiary motifNucleic acid structureMotif search |
| spellingShingle | Eugene F. Baulin Davyd R. Bohdan Dawid Kowalski Milena Serwatka Julia Świerczyńska Zuzanna Żyra Janusz M. Bujnicki ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations Genome Biology Kink-turn K-junction A-minor junction Tertiary motif Nucleic acid structure Motif search |
| title | ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations |
| title_full | ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations |
| title_fullStr | ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations |
| title_full_unstemmed | ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations |
| title_short | ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations |
| title_sort | artem a method for rna and dna tertiary motif identification with backbone permutations |
| topic | Kink-turn K-junction A-minor junction Tertiary motif Nucleic acid structure Motif search |
| url | https://doi.org/10.1186/s13059-025-03696-2 |
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