{"doi":"10.1021/acs.jcim.4c00756","title":"Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment","abstract":"Ribonucleic acid (RNA) molecules can adopt a variety of secondary and tertiary structures in solution, with stem-loops being one of the more common motifs. Here, we present a systematic analysis of 15 RNA stem-loop sequences simulated with molecular dynamics simulations in an implicit solvent environment. Analysis of RNA cluster ensembles showed that the stem-loop structures can generally adopt the A-form RNA in the stem region. Loop structures are more sensitive, and experimental structures could only be reproduced with modification of CH···O interactions in the force field, combined with an implicit solvent nonpolar correction to better model base stacking interactions. Accurately modeling RNA with current atomistic physics-based models remains challenging, but the RNA systems studied herein may provide a useful benchmark set for testing other RNA modeling methods in the future.","journal":"Journal of Chemical Information and Modeling","year":2024,"id":465931,"datarank":0.24141568686511508,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"self_citation_contribution":0.24141568686511508,"citation_network_contribution":0.0,"self_endowment_contribution":0.24141568686511508,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9595,"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":1297317,"name":"Ethan Aminov","orcid":"0009-0003-2787-1869","position":1,"is_corresponding":false},{"id":1297752,"name":"Aalim S. Abdullah","orcid":null,"position":2,"is_corresponding":false},{"id":1297318,"name":"Colleen Kirkup","orcid":"0009-0008-4313-5358","position":3,"is_corresponding":false},{"id":1297319,"name":"Rebeca I. Diaz Ventura","orcid":"0009-0006-0207-3053","position":4,"is_corresponding":false},{"id":1297320,"name":"Vinay R. Bijoor","orcid":"0009-0009-5837-376X","position":5,"is_corresponding":false},{"id":1297753,"name":"Jiyun Jung","orcid":null,"position":6,"is_corresponding":false},{"id":1297321,"name":"S. L. Huang","orcid":"0009-0003-4838-9916","position":7,"is_corresponding":false},{"id":1297754,"name":"Chi Gee Tse","orcid":null,"position":8,"is_corresponding":false},{"id":1297755,"name":"Emily Álvarez Toucet","orcid":null,"position":9,"is_corresponding":false},{"id":1297322,"name":"Hugo P. Onghai","orcid":"0009-0006-7779-0380","position":10,"is_corresponding":false},{"id":1297323,"name":"Arghya Ghosh","orcid":"0000-0002-0780-9780","position":11,"is_corresponding":false},{"id":1297324,"name":"Alex C. Grodzki","orcid":"0009-0007-7041-9041","position":12,"is_corresponding":false},{"id":1297756,"name":"Emilee R. Haines","orcid":null,"position":13,"is_corresponding":false},{"id":1297325,"name":"Aditya Iyer","orcid":"0000-0002-3144-6385","position":14,"is_corresponding":false},{"id":1297326,"name":"Mark K. Khalil","orcid":"0009-0003-4380-229X","position":15,"is_corresponding":false},{"id":1297327,"name":"Alexander P. Leong","orcid":"0009-0005-2693-7496","position":16,"is_corresponding":false},{"id":1297757,"name":"Michael A. Neuhaus","orcid":null,"position":17,"is_corresponding":false},{"id":1297328,"name":"Joseph Park","orcid":"0009-0006-5241-7715","position":18,"is_corresponding":false},{"id":1297329,"name":"Asir Shahid","orcid":"0009-0009-6232-387X","position":19,"is_corresponding":false},{"id":1297758,"name":"Matthew Xie","orcid":null,"position":20,"is_corresponding":false},{"id":1297759,"name":"Jan M. Ziembicki","orcid":null,"position":21,"is_corresponding":false},{"id":39812,"name":"Carlos Simmerling","orcid":"0000-0002-7252-4730","position":22,"is_corresponding":false},{"id":1013588,"name":"Maria C. Nagan","orcid":"0000-0003-2678-6825","position":23,"is_corresponding":false},{"id":1297316,"name":"Jason Linzer","orcid":"0009-0008-2739-5432","position":0,"is_corresponding":true}],"reference_count":89,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:04:50.328230Z","pmid":"39002142","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":[]}