{"doi":"10.17615/7e3c-mv82","title":"RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone","abstract":"Although accurate details in RNA structure are of great importance for understanding RNA function, the backbone conformation is difficult to determine, and most existing RNA structures show serious steric clashes (≥ 0.4Å overlap) when hydrogen atoms are taken into account. We have developed a program called RNABC (RNA Backbone Correction) that performs local perturbations to search for alternative conformations that avoid those steric clashes or other local geometry problems. Its input is an all-atom coordinate file for an RNA crystal structure (usually from the MolProbity web service), with problem areas specified. RNABC rebuilds a suite (the unit from sugar to sugar) by anchoring the phosphorus and base positions, which are clearest in crystallographic electron density, and reconstructing the other atoms using forward kinematics. Geometric parameters are constrained within user-specified tolerance of canonical or original values, and torsion angles are constrained to ranges defined through empirical database analyses. Several optimizations reduce the time required to search the many possible conformations. The output results are clustered and presented to the user, who can choose whether to accept one of the alternative conformations.","journal":"UNC Libraries","year":2020,"id":117685,"datarank":0.23085142246483747,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.12687934538084567,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.12687934538084567,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":1,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9581,"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":548353,"name":"Xueyi Wang","orcid":"0009-0002-8072-1766","position":1,"is_corresponding":false},{"id":548354,"name":"David Richardson","orcid":"0000-0003-0247-9118","position":2,"is_corresponding":false},{"id":548355,"name":"Jack Snoeyink","orcid":"0000-0002-3887-4008","position":3,"is_corresponding":false},{"id":55082,"name":"Jane S. Richardson","orcid":"0000-0002-3311-2944","position":4,"is_corresponding":false},{"id":481072,"name":"Laura Murray","orcid":"0000-0002-0492-6906","position":5,"is_corresponding":false},{"id":55080,"name":"Gary J. Kapral","orcid":null,"position":0,"is_corresponding":true}],"reference_count":0,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-18T23:13:54.951170Z","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":[]}