{"doi":"10.1101/2024.03.15.585203","title":"HUHgle: An Interactive Substrate Design Tool for Covalent Protein-ssDNA Labeling Using HUH-tags","abstract":"Abstract HUH-tags have emerged as versatile fusion partners that mediate sequence specific protein-ssDNA bioconjugation through a simple and efficient reaction. Here we present HUHgle, a python-based interactive tool for the visualization, design, and optimization of substrates for HUH-tag mediated covalent labeling of proteins of interest with ssDNA substrates of interest. HUHgle streamlines design processes by integrating an intuitive plotting interface with a search function capable of predicting and displaying protein-ssDNA bioconjugate formation efficiency and specificity in proposed HUH-tag/ssDNA sequence combinations. Validation demonstrates that HUHgle accurately predicts product formation of HUH-tag mediated bioconjugation for single- and orthogonal-labeling reactions. In order to maximize the accessibility and utility of HUHgle, we have implemented it as a user-friendly Google Colab notebook which facilitates broad use of this tool, regardless of coding expertise. Graphical Abstract","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":490391,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9516,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1130525,"name":"Natalia S. Babilonia-Díaz","orcid":null,"position":1,"is_corresponding":false},{"id":1283666,"name":"Aspen J. Hughes","orcid":null,"position":2,"is_corresponding":false},{"id":1283667,"name":"Andrew C. D. Lemmex","orcid":null,"position":3,"is_corresponding":false},{"id":821382,"name":"Michael J. Anderson","orcid":"0000-0001-5116-1427","position":4,"is_corresponding":false},{"id":329583,"name":"Kassidy J. Tompkins","orcid":"0000-0003-0427-2671","position":5,"is_corresponding":false},{"id":329591,"name":"Wendy R. Gordon","orcid":"0000-0001-7696-5560","position":6,"is_corresponding":false},{"id":1010777,"name":"Adam T. Smiley","orcid":"0000-0002-3891-8242","position":0,"is_corresponding":true}],"reference_count":24,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:08:37.162700Z","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":[]}