{"doi":"10.1016/j.molcel.2023.06.019","title":"HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence","abstract":"RNA-binding proteins (RBPs) control RNA metabolism to orchestrate gene expression and, when dysfunctional, underlie human diseases. Proteome-wide discovery efforts predict thousands of RBP candidates, many of which lack canonical RNA-binding domains (RBDs). Here, we present a hybrid ensemble RBP classifier (HydRA), which leverages information from both intermolecular protein interactions and internal protein sequence patterns to predict RNA-binding capacity with unparalleled specificity and sensitivity using support vector machines (SVMs), convolutional neural networks (CNNs), and Transformer-based protein language models. Occlusion mapping by HydRA robustly detects known RBDs and predicts hundreds of uncharacterized RNA-binding associated domains. Enhanced CLIP (eCLIP) for HydRA-predicted RBP candidates reveals transcriptome-wide RNA targets and confirms RNA-binding activity for HydRA-predicted RNA-binding associated domains. HydRA accelerates construction of a comprehensive RBP catalog and expands the diversity of RNA-binding associated domains.","journal":"Molecular Cell","year":2023,"id":320091,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":51,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9492,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":461477,"name":"Kristopher W. Brannan","orcid":"0000-0002-0316-898X","position":1,"is_corresponding":false},{"id":1030461,"name":"Katannya Kapeli","orcid":null,"position":2,"is_corresponding":false},{"id":660020,"name":"Samuel S. Park","orcid":"0000-0002-9230-7661","position":3,"is_corresponding":false},{"id":129454,"name":"Hui Tan","orcid":null,"position":4,"is_corresponding":false},{"id":418342,"name":"Maya L. Gosztyla","orcid":"0000-0003-4758-4800","position":5,"is_corresponding":false},{"id":1030462,"name":"Mayuresh Mujumdar","orcid":null,"position":6,"is_corresponding":false},{"id":1030463,"name":"Joshua Ahdout","orcid":null,"position":7,"is_corresponding":false},{"id":1030464,"name":"Bryce Henroid","orcid":null,"position":8,"is_corresponding":false},{"id":21632,"name":"Katherine Rothamel","orcid":"0000-0001-9896-485X","position":9,"is_corresponding":false},{"id":567103,"name":"Joy S. Xiang","orcid":"0000-0002-6400-1876","position":10,"is_corresponding":false},{"id":1030011,"name":"Limsoon Wong","orcid":"0000-0003-1241-5441","position":11,"is_corresponding":false},{"id":43290,"name":"G Yeo","orcid":null,"position":12,"is_corresponding":false},{"id":236070,"name":"Wenhao Jin","orcid":"0000-0002-7885-3527","position":0,"is_corresponding":true}],"reference_count":84,"raw_metadata":null,"created_at":"2026-07-19T01:07:17.361058Z","pmid":"37421941","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":[]}