{"doi":"10.1128/msystems.00267-20","title":"RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery","abstract":"Bioinformatics-powered discovery of novel ribosomal natural products (RiPPs) has historically been hindered by the lack of a common genetic feature across RiPP classes. Herein, we introduce RRE-Finder, a method for identifying RRE domains, which are present in a majority of prokaryotic RiPP biosynthetic gene clusters (BGCs). RRE-Finder identifies RRE domains 3,000 times faster than current methods, which rely on time-consuming secondary structure prediction. Depending on user goals, RRE-Finder can operate in precision mode to accurately identify RREs present in known RiPP classes or in exploratory mode to assist with novel RiPP discovery. Employing RRE-Finder on the UniProtKB database revealed several high-confidence RREs in novel RiPP-like clusters, suggesting that many new RiPP classes remain to be discovered.","journal":"mSystems","year":2020,"id":53660,"datarank":2.9300207397968374,"base_score":4.74493212836325,"endowment":4.74493212836325,"self_citation_contribution":0.7117398192544876,"citation_network_contribution":2.21828092054235,"self_endowment_contribution":0.7117398192544876,"citer_contribution":2.21828092054235,"corpus_percentile":null,"corpus_rank":null,"citation_count":114,"citer_count":92,"citers_with_citation_signal":78,"citers_with_endowment":78,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9621,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":274282,"name":"Kyle E. Shelton","orcid":"0000-0002-9887-929X","position":1,"is_corresponding":false},{"id":274283,"name":"Gilles P. van Wezel","orcid":"0000-0003-0341-1561","position":2,"is_corresponding":false},{"id":36673,"name":"Marnix H. Medema","orcid":"0000-0002-2191-2821","position":3,"is_corresponding":false},{"id":256349,"name":"Douglas A. Mitchell","orcid":"0000-0002-9564-0953","position":4,"is_corresponding":false},{"id":274281,"name":"Alexander Kloosterman","orcid":"0000-0001-7345-110X","position":0,"is_corresponding":true}],"reference_count":60,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-18T20:45:25.145885Z","pmid":"32873609","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":[]}