{"id":"https://openalex.org/W7222895313","doi":"https://doi.org/10.64898/2026.10.15.759315","title":"LigRNA: High-accuracy prediction of RNA-ligand binding sites via dynamic chemical complementarity and language model encoding","display_name":"LigRNA: High-accuracy prediction of RNA-ligand binding sites via dynamic chemical complementarity and language model encoding","publication_year":2026,"publication_date":"2026-10-17","ids":{"openalex":"https://openalex.org/W7222895313","doi":"https://doi.org/10.64898/2026.10.15.759315"},"language":"en","primary_location":{"id":"doi:10.64898/2026.10.15.759315","doi":"https://doi.org/10.64898/2026.10.15.759315","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.15.759315","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/17/2026.10.15.759315.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/17/2026.10.15.759315.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5159019952","display_name":"Xin Wang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xin Wang","raw_affiliation_strings":["Medical Imaging, Robotics, Analytic Computing & Learning (MIRACLE) Lab, YRD-RIGHT, Suzhou Institute for Advance Research, USTC, Jiangsu, 215123, China","School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, 230026, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Imaging, Robotics, Analytic Computing & Learning (MIRACLE) Lab, YRD-RIGHT, Suzhou Institute for Advance Research, USTC, Jiangsu, 215123, China","institution_ids":[]},{"raw_affiliation_string":"School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, 230026, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021646701","display_name":"Heqin Zhu","orcid":"https://orcid.org/0000-0001-9469-950X","observed_orcids":["https://orcid.org/0000-0001-9469-950X"]},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Heqin Zhu","raw_affiliation_strings":["Medical Imaging, Robotics, Analytic Computing & Learning (MIRACLE) Lab, YRD-RIGHT, Suzhou Institute for Advance Research, USTC, Jiangsu, 215123, China","School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, 230026, China"],"raw_orcid":"https://orcid.org/0000-0001-9469-950X","affiliations":[{"raw_affiliation_string":"Medical Imaging, Robotics, Analytic Computing & Learning (MIRACLE) Lab, YRD-RIGHT, Suzhou Institute for Advance Research, USTC, Jiangsu, 215123, China","institution_ids":[]},{"raw_affiliation_string":"School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, 230026, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5159009165","display_name":"Hao Li","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hao Li","raw_affiliation_strings":["Medical Imaging, Robotics, Analytic Computing & Learning (MIRACLE) Lab, YRD-RIGHT, Suzhou Institute for Advance Research, USTC, Jiangsu, 215123, China","School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, 230026, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Imaging, Robotics, Analytic Computing & Learning (MIRACLE) Lab, YRD-RIGHT, Suzhou Institute for Advance Research, USTC, Jiangsu, 215123, China","institution_ids":[]},{"raw_affiliation_string":"School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, 230026, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135880141","display_name":"Ao Chang","orcid":"https://orcid.org/0009-0002-2526-5649","observed_orcids":["https://orcid.org/0009-0002-2526-5649"]},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ao Chang","raw_affiliation_strings":["Medical Imaging, Robotics, Analytic Computing & Learning (MIRACLE) Lab, YRD-RIGHT, Suzhou Institute for Advance Research, USTC, Jiangsu, 215123, China","School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, 230026, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Imaging, Robotics, Analytic Computing & Learning (MIRACLE) Lab, YRD-RIGHT, Suzhou Institute for Advance Research, USTC, Jiangsu, 215123, China","institution_ids":[]},{"raw_affiliation_string":"School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, 230026, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5159021639","display_name":"Feng Zhang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Feng Zhang","raw_affiliation_strings":["Medical Imaging, Robotics, Analytic Computing & Learning (MIRACLE) Lab, YRD-RIGHT, Suzhou Institute for Advance Research, USTC, Jiangsu, 215123, China","School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, 230026, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Imaging, Robotics, Analytic Computing & Learning (MIRACLE) Lab, YRD-RIGHT, Suzhou Institute for Advance Research, USTC, Jiangsu, 215123, China","institution_ids":[]},{"raw_affiliation_string":"School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, 230026, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138546137","display_name":"Haobin Chen","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haobin Chen","raw_affiliation_strings":["Medical Imaging, Robotics, Analytic Computing & Learning (MIRACLE) Lab, YRD-RIGHT, Suzhou Institute for Advance Research, USTC, Jiangsu, 215123, China","School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, 230026, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Imaging, Robotics, Analytic Computing & Learning (MIRACLE) Lab, YRD-RIGHT, Suzhou Institute for Advance Research, USTC, Jiangsu, 215123, China","institution_ids":[]},{"raw_affiliation_string":"School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, 230026, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5150711700","display_name":"Chenxi Wang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chenxi Wang","raw_affiliation_strings":["Medical Imaging, Robotics, Analytic Computing & Learning (MIRACLE) Lab, YRD-RIGHT, Suzhou Institute for Advance Research, USTC, Jiangsu, 215123, China","School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, 230026, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Imaging, Robotics, Analytic Computing & Learning (MIRACLE) Lab, YRD-RIGHT, Suzhou Institute for Advance Research, USTC, Jiangsu, 215123, China","institution_ids":[]},{"raw_affiliation_string":"School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, 230026, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5159021586","display_name":"Ke Chen","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ke Chen","raw_affiliation_strings":["Medical Imaging, Robotics, Analytic Computing & Learning (MIRACLE) Lab, YRD-RIGHT, Suzhou Institute for Advance Research, USTC, Jiangsu, 215123, China","School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, 230026, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Imaging, Robotics, Analytic Computing & Learning (MIRACLE) Lab, YRD-RIGHT, Suzhou Institute for Advance Research, USTC, Jiangsu, 215123, China","institution_ids":[]},{"raw_affiliation_string":"School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, 230026, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5159025732","display_name":"S Kevin Zhou","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shaohua Kevin Zhou","raw_affiliation_strings":["Biomedical Basic Research Center (BBRC) of Jiangsu, Jiangsu, 215123, China","Jiangsu Key Laboratory of Multimodal Digital Twin Technology, Jiangsu, 215123, China","Medical Imaging, Robotics, Analytic Computing & Learning (MIRACLE) Lab, YRD-RIGHT, Suzhou Institute for Advance Research, USTC, Jiangsu, 215123, China","School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, 230026, China","State Key Laboratory of Precision and Intelligent Chemistry, Anhui, 230026, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Basic Research Center (BBRC) of Jiangsu, Jiangsu, 215123, China","institution_ids":[]},{"raw_affiliation_string":"Jiangsu Key Laboratory of Multimodal Digital Twin Technology, Jiangsu, 215123, China","institution_ids":[]},{"raw_affiliation_string":"Medical Imaging, Robotics, Analytic Computing & Learning (MIRACLE) Lab, YRD-RIGHT, Suzhou Institute for Advance Research, USTC, Jiangsu, 215123, China","institution_ids":[]},{"raw_affiliation_string":"School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, 230026, China","institution_ids":["https://openalex.org/I126520041"]},{"raw_affiliation_string":"State Key Laboratory of Precision and Intelligent Chemistry, Anhui, 230026, China","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026473554","display_name":"Peng Xiong","orcid":"https://orcid.org/0000-0002-5888-377X","observed_orcids":["https://orcid.org/0000-0002-5888-377X"]},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Peng Xiong","raw_affiliation_strings":["Biomedical Basic Research Center (BBRC) of Jiangsu, Jiangsu, 215123, China","Medical Imaging, Robotics, Analytic Computing & Learning (MIRACLE) Lab, YRD-RIGHT, Suzhou Institute for Advance Research, USTC, Jiangsu, 215123, China","School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, 230026, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Basic Research Center (BBRC) of Jiangsu, Jiangsu, 215123, China","institution_ids":[]},{"raw_affiliation_string":"Medical Imaging, Robotics, Analytic Computing & Learning (MIRACLE) Lab, YRD-RIGHT, Suzhou Institute for Advance Research, USTC, Jiangsu, 215123, China","institution_ids":[]},{"raw_affiliation_string":"School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, 230026, China","institution_ids":["https://openalex.org/I126520041"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5026473554"],"corresponding_institution_ids":["https://openalex.org/I126520041"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.7904999852180481,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.7904999852180481,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.17069999873638153,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.006099999882280827,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/rna-binding-small-molecules","display_name":"RNA-binding small molecules","score":0.9279999732971191},{"id":"https://openalex.org/keywords/graph-neural-networks","display_name":"graph neural networks","score":0.7620000243186951},{"id":"https://openalex.org/keywords/language-model-embeddings","display_name":"language model embeddings","score":0.7599999904632568},{"id":"https://openalex.org/keywords/graph-attention-networks","display_name":"graph attention networks","score":0.6959999799728394},{"id":"https://openalex.org/keywords/cross-attention","display_name":"cross-attention","score":0.8379999995231628},{"id":"https://openalex.org/keywords/rna-secondary-structure","display_name":"RNA secondary structure","score":0.5170000195503235},{"id":"https://openalex.org/keywords/solvent-accessible-surface-area","display_name":"solvent accessible surface area","score":0.9419999718666077},{"id":"https://openalex.org/keywords/rna-targeted-drug-design","display_name":"RNA-targeted drug design","score":0.5759999752044678}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5981000065803528},{"id":"https://openalex.org/C202269582","wikidata":"https://www.wikidata.org/wiki/Q2644277","display_name":"Complementarity (molecular biology)","level":2,"score":0.5608000159263611},{"id":"https://openalex.org/C87619178","wikidata":"https://www.wikidata.org/wiki/Q126002","display_name":"Concatenation (mathematics)","level":2,"score":0.555400013923645},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.517799973487854},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5077999830245972},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.49380001425743103},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4812999963760376},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.43459999561309814},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.400299996137619},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.3977000117301941},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.3779999911785126},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.3700000047683716},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.36880001425743103},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.35100001096725464},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.3463999927043915},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.33180001378059387},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.3028999865055084},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.2904999852180481},{"id":"https://openalex.org/C146380142","wikidata":"https://www.wikidata.org/wiki/Q1137726","display_name":"Directed graph","level":2,"score":0.28529998660087585},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.28189998865127563},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.2806999981403351},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.27639999985694885},{"id":"https://openalex.org/C57273362","wikidata":"https://www.wikidata.org/wiki/Q576722","display_name":"Decoding methods","level":2,"score":0.2646999955177307},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.25619998574256897}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.10.15.759315","doi":"https://doi.org/10.64898/2026.10.15.759315","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.15.759315","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/17/2026.10.15.759315.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.10.15.759315","doi":"https://doi.org/10.64898/2026.10.15.759315","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.15.759315","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/17/2026.10.15.759315.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2194546774","display_name":null,"funder_award_id":"32370581","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7571408944","display_name":null,"funder_award_id":"62271465","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7222895313.pdf","grobid_xml":"https://content.openalex.org/works/W7222895313.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1966716734","https://openalex.org/W2038093560","https://openalex.org/W2055043387","https://openalex.org/W2102245393","https://openalex.org/W2156125289","https://openalex.org/W2170505850","https://openalex.org/W2339718724","https://openalex.org/W2418483870","https://openalex.org/W2620760558","https://openalex.org/W2747225324","https://openalex.org/W2799691204","https://openalex.org/W2820941669","https://openalex.org/W2951298881","https://openalex.org/W2963351448","https://openalex.org/W3092622323","https://openalex.org/W3104537585","https://openalex.org/W3118778953","https://openalex.org/W3126232929","https://openalex.org/W3211077113","https://openalex.org/W4309362395","https://openalex.org/W4393055202","https://openalex.org/W4402567383","https://openalex.org/W4407597143","https://openalex.org/W4410997423","https://openalex.org/W4411882193","https://openalex.org/W4413120297"],"related_works":["https://openalex.org/W4413140665","https://openalex.org/W4413105138","https://openalex.org/W4309362395","https://openalex.org/W7213653462","https://openalex.org/W4411924972","https://openalex.org/W7122778885","https://openalex.org/W7211950571","https://openalex.org/W4409628391","https://openalex.org/W4407597143","https://openalex.org/W4396853218"],"abstract_inverted_index":{"Abstract":[0],"RNA-binding":[1],"small":[2],"molecules":[3,112],"represent":[4],"a":[5,57],"validated":[6],"therapeutic":[7],"modality,":[8],"yet":[9],"pinpointing":[10],"their":[11],"exact":[12],"RNA":[13,47,92,125,158],"binding":[14,65],"sites":[15,66],"remains":[16],"critical":[17],"for":[18],"mechanistic":[19],"understanding":[20],"and":[21,30,49,85,135,144,151],"drug":[22],"optimization.":[23],"Experimental":[24],"methods,":[25],"while":[26],"precise,":[27],"are":[28,95],"costly":[29],"low-throughput,":[31],"necessitating":[32],"robust":[33],"computational":[34],"alternatives.":[35],"Approaches":[36],"based":[37],"on":[38,133,147],"static":[39],"feature":[40],"concatenation":[41],"may":[42],"overlook":[43],"input-dependent":[44],"relationships":[45],"between":[46],"residues":[48],"ligand":[50],"functional":[51],"groups.":[52],"Here":[53],"we":[54],"present":[55],"LigRNA,":[56],"graph":[58,102],"neural":[59],"network":[60],"framework":[61],"that":[62],"predicts":[63],"RNA-ligand":[64],"through":[67],"joint":[68],"cross-modal":[69],"encoding":[70],"of":[71,124,142],"both":[72],"molecules.":[73],"LigRNA":[74,138],"integrates":[75],"structure-guided":[76],"language":[77],"model":[78],"embeddings":[79],"with":[80],"physicochemical":[81],"features-solvent-accessible":[82],"surface":[83],"area":[84],"secondary":[86],"structure":[87],"types,":[88],"to":[89],"construct":[90],"comprehensive":[91],"representations.":[93],"Ligands":[94],"encoded":[96],"as":[97,161],"attributed":[98],"molecular":[99],"graphs":[100],"via":[101],"attention":[103],"networks,":[104],"preserving":[105],"atom-level":[106],"chemical":[107],"topology":[108],"rather":[109],"than":[110],"compressing":[111],"into":[113],"fixed":[114],"fingerprints.":[115],"A":[116],"cross-attention":[117],"mechanism":[118],"then":[119],"enables":[120],"dynamic,":[121],"ligand-dependent":[122],"modulation":[123],"nucleotide":[126],"attention,":[127],"capturing":[128],"context-specific":[129],"interaction":[130],"patterns.":[131],"Benchmarked":[132],"TE9":[134],"TE18":[136],"datasets,":[137],"achieves":[139],"F1":[140],"scores":[141],"0.73":[143],"0.58,":[145],"improving":[146],"GATRsite":[148],"by":[149],"7.4%":[150],"18.4%,":[152],"respectively.":[153],"Ablation":[154],"studies":[155],"identify":[156],"the":[157,162,167],"residual":[159],"encoder":[160],"most":[163],"consistent":[164],"contributor":[165],"across":[166],"two":[168],"benchmarks.":[169],"The":[170],"source":[171],"code":[172],"is":[173],"freely":[174],"available":[175],"at":[176],"https://github.com/WillowWang0216/LigRNA":[177],".":[178]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-10-19T00:00:00"}