{"doi":"10.1093/bioinformatics/bty404","title":"SSMART: sequence-structure motif identification for RNA-binding proteins","abstract":"<jats:title>Abstract</jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation</jats:title>\n                    <jats:p>RNA-binding proteins (RBPs) regulate every aspect of RNA metabolism and function. There are hundreds of RBPs encoded in the eukaryotic genomes, and each recognize its RNA targets through a specific mixture of RNA sequence and structure properties. For most RBPs, however, only a primary sequence motif has been determined, while the structure of the binding sites is uncharacterized.</jats:p>\n                  </jats:sec>\n                  <jats:sec>\n                    <jats:title>Results</jats:title>\n                    <jats:p>We developed SSMART, an RNA motif finder that simultaneously models the primary sequence and the structural properties of the RNA targets sites. The sequence-structure motifs are represented as consensus strings over a degenerate alphabet, extending the IUPAC codes for nucleotides to account for secondary structure preferences. Evaluation on synthetic data showed that SSMART is able to recover both sequence and structure motifs implanted into 3′UTR-like sequences, for various degrees of structured/unstructured binding sites. In addition, we successfully used SSMART on high-throughput in vivo and in vitro data, showing that we not only recover the known sequence motif, but also gain insight into the structural preferences of the RBP.</jats:p>\n                  </jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation</jats:title>\n                    <jats:p>SSMART is freely available at https://ohlerlab.mdc-berlin.de/software/SSMART_137/.</jats:p>\n                  </jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information</jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.</jats:p>\n                  </jats:sec>","journal":"Bioinformatics","year":2018,"id":636738,"datarank":0.4943755299006494,"base_score":3.295836866004329,"endowment":3.295836866004329,"self_citation_contribution":0.4943755299006494,"citation_network_contribution":0.0,"self_endowment_contribution":0.4943755299006494,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":26,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":211247,"name":"Neelanjan Mukherjee","orcid":null,"position":1,"is_corresponding":false},{"id":28491,"name":"Uwe Ohler","orcid":"0000-0002-0881-3116","position":2,"is_corresponding":false},{"id":666954,"name":"Alina Munteanu","orcid":"0000-0001-5917-3246","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"SSMART: sequence-structure motif identification for RNA-binding proteins","abstract":"<jats:title>Abstract</jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation</jats:title>\n                    <jats:p>RNA-binding proteins (RBPs) regulate every aspect of RNA metabolism and function. There are hundreds of RBPs encoded in the eukaryotic genomes, and each recognize its RNA targets through a specific mixture of RNA sequence and structure properties. For most RBPs, however, only a primary sequence motif has been determined, while the structure of the binding sites is uncharacterized.</jats:p>\n                  </jats:sec>\n                  <jats:sec>\n                    <jats:title>Results</jats:title>\n                    <jats:p>We developed SSMART, an RNA motif finder that simultaneously models the primary sequence and the structural properties of the RNA targets sites. The sequence-structure motifs are represented as consensus strings over a degenerate alphabet, extending the IUPAC codes for nucleotides to account for secondary structure preferences. Evaluation on synthetic data showed that SSMART is able to recover both sequence and structure motifs implanted into 3′UTR-like sequences, for various degrees of structured/unstructured binding sites. In addition, we successfully used SSMART on high-throughput in vivo and in vitro data, showing that we not only recover the known sequence motif, but also gain insight into the structural preferences of the RBP.</jats:p>\n                  </jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation</jats:title>\n                    <jats:p>SSMART is freely available at https://ohlerlab.mdc-berlin.de/software/SSMART_137/.</jats:p>\n                  </jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information</jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.</jats:p>\n                  </jats:sec>","is_dataset_classified":null,"base_score":3.295836866004329,"endowment":3.295836866004329,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"29893814","pmcid":"PMC6247937","openalex_id":"https://openalex.org/W2751343946","authors":[],"funders":[{"funder_name":"National Institutes of Health","grant_id":"R01-GM104962","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"R01 GM104962","title":null},{"funder_name":"National Institutes of Health","grant_id":"5R01GM104962-02","title":"Posttranscriptional regulation by mRNA-binding shuttling and transport proteins"}],"total_grants":3,"fwci":1.6496,"citation_percentile":0.83797817,"influential_citations":0,"citation_trend":[{"year":2018,"count":3},{"year":2019,"count":5},{"year":2020,"count":4},{"year":2021,"count":8},{"year":2022,"count":3},{"year":2024,"count":2},{"year":2025,"count":1}],"oa_status":"bronze","license":"OUP Standard Publication Reuse","oa_locations":[{"url":"https://academic.oup.com/bioinformatics/article-pdf/34/23/3990/26676728/bty404.pdf","host_type":"journal"},{"url":"https://academic.oup.com/bioinformatics/article-pdf/34/23/3990/26676728/bty404.pdf","host_type":"publisher"},{"url":"https://academic.oup.com/bioinformatics/article-pdf/34/23/3990/48921027/bioinformatics_34_23_3990.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/bioinformatics/bty404","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/29893814","host_type":"repository"},{"url":"https://edoc.mdc-berlin.de/17497/","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6247937","host_type":"repository"},{"url":"https://doi.org/10.7490/f1000research.1114604.1","host_type":""},{"url":"https://dx.doi.org/10.7490/f1000research.1114604.1","host_type":""},{"url":"https://doi.org/10.1101/287953","host_type":""},{"url":"https://dx.doi.org/10.1093/bioinformatics/bty404","host_type":""},{"url":"https://dx.doi.org/10.1101/287953","host_type":""},{"url":"http://dx.doi.org/10.1101/287953","host_type":""}],"fields_of_study":["RNA Research and Splicing","RNA and protein synthesis mechanisms","RNA modifications and cancer","0301 basic medicine","0303 health sciences","03 medical and health sciences"],"mesh_terms":["Binding Sites","RNA","Software","RNA-Binding Proteins","Sequence Analysis, RNA","Computational Biology","Nucleotide Motifs"],"keywords":["RNA","Computational biology","Sequence motif","Nucleic acid structure","Structural motif","RNA-binding protein","Biology","Nucleic acid secondary structure","Riboswitch","Sequence (biology)","Consensus sequence","Motif (music)","RNA recognition motif","Protein secondary structure","Genetics","DNA","Non-coding RNA","Peptide sequence","Gene","Biochemistry","Binding Sites","Sequence Analysis, RNA","RNA-Binding Proteins","Nucleotide Motifs","Software"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-06T17:38:49.238273Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}