{"id":"https://openalex.org/W4404249429","doi":"https://doi.org/10.1021/acs.jcim.4c01621","title":"lociPARSE: A Locality-aware Invariant Point Attention Model for Scoring RNA 3D Structures","display_name":"lociPARSE: A Locality-aware Invariant Point Attention Model for Scoring RNA 3D Structures","publication_year":2024,"publication_date":"2024-11-11","ids":{"openalex":"https://openalex.org/W4404249429","doi":"https://doi.org/10.1021/acs.jcim.4c01621","pmid":"https://pubmed.ncbi.nlm.nih.gov/39523843"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c01621","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01621","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c01621?ref=article_openPDF","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c01621?ref=article_openPDF","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029120254","display_name":"Sumit Tarafder","orcid":null},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sumit Tarafder","raw_affiliation_strings":["Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, United States","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018409409","display_name":"Debswapna Bhattacharya","orcid":"https://orcid.org/0000-0002-9630-0141"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Debswapna Bhattacharya","raw_affiliation_strings":["Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, United States"],"raw_orcid":"https://orcid.org/0000-0002-9630-0141","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, United States","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5018409409"],"corresponding_institution_ids":["https://openalex.org/I859038795"],"apc_list":null,"apc_paid":null,"fwci":2.1929,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.8822013,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"64","issue":"22","first_page":"8655","last_page":"8664"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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/T10604","display_name":"RNA Research and Splicing","score":0.9990000128746033,"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/T11482","display_name":"RNA modifications and cancer","score":0.9988999962806702,"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/locality","display_name":"Locality","score":0.7929823398590088},{"id":"https://openalex.org/keywords/invariant","display_name":"Invariant (physics)","score":0.7261705994606018},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45473936200141907},{"id":"https://openalex.org/keywords/point","display_name":"Point (geometry)","score":0.4437263607978821},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33064448833465576},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.32293641567230225},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.1525060534477234},{"id":"https://openalex.org/keywords/mathematical-physics","display_name":"Mathematical physics","score":0.14987993240356445}],"concepts":[{"id":"https://openalex.org/C2779808786","wikidata":"https://www.wikidata.org/wiki/Q6664603","display_name":"Locality","level":2,"score":0.7929823398590088},{"id":"https://openalex.org/C190470478","wikidata":"https://www.wikidata.org/wiki/Q2370229","display_name":"Invariant (physics)","level":2,"score":0.7261705994606018},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45473936200141907},{"id":"https://openalex.org/C28719098","wikidata":"https://www.wikidata.org/wiki/Q44946","display_name":"Point (geometry)","level":2,"score":0.4437263607978821},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33064448833465576},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.32293641567230225},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.1525060534477234},{"id":"https://openalex.org/C37914503","wikidata":"https://www.wikidata.org/wiki/Q156495","display_name":"Mathematical physics","level":1,"score":0.14987993240356445},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jcim.4c01621","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01621","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c01621?ref=article_openPDF","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:39523843","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39523843","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:vtechworks.lib.vt.edu:10919/138170","is_oa":true,"landing_page_url":"https://hdl.handle.net/10919/138170","pdf_url":"https://vtechworks.lib.vt.edu/bitstreams/d41282a5-338b-4e8e-a438-e1f5d138f4ea/download","source":{"id":"https://openalex.org/S4306400248","display_name":"VTechWorks (Virginia Tech)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I859038795","host_organization_name":"Virginia Tech","host_organization_lineage":["https://openalex.org/I859038795"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:11600500","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11600500","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11600500/pdf/ci4c01621.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.4c01621","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01621","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c01621?ref=article_openPDF","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3741541039","display_name":null,"funder_award_id":"R35 GM138146","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3891976813","display_name":null,"funder_award_id":"R35GM138146","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G532746849","display_name":null,"funder_award_id":"DBI2208679","funder_id":"https://openalex.org/F4320337398","funder_display_name":"Division of Biological Infrastructure"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337398","display_name":"Division of Biological Infrastructure","ror":"https://ror.org/04qn9mx93"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4404249429.pdf"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1724277458","https://openalex.org/W1976961172","https://openalex.org/W1980155855","https://openalex.org/W1999613945","https://openalex.org/W2017838368","https://openalex.org/W2047026361","https://openalex.org/W2052963427","https://openalex.org/W2097511300","https://openalex.org/W2102591917","https://openalex.org/W2103894153","https://openalex.org/W2111652614","https://openalex.org/W2116687527","https://openalex.org/W2117451312","https://openalex.org/W2119896557","https://openalex.org/W2125677968","https://openalex.org/W2137736208","https://openalex.org/W2140673705","https://openalex.org/W2149605074","https://openalex.org/W2151581834","https://openalex.org/W2161776897","https://openalex.org/W2170747616","https://openalex.org/W2341963847","https://openalex.org/W2342307854","https://openalex.org/W2554722417","https://openalex.org/W2902320679","https://openalex.org/W2980444668","https://openalex.org/W2981760759","https://openalex.org/W3022554208","https://openalex.org/W3177828909","https://openalex.org/W3183772760","https://openalex.org/W3195820203","https://openalex.org/W3213615006","https://openalex.org/W4212774754","https://openalex.org/W4280513900","https://openalex.org/W4293475204","https://openalex.org/W4310568385","https://openalex.org/W4323076291","https://openalex.org/W4380291688","https://openalex.org/W4385068123","https://openalex.org/W4386804219","https://openalex.org/W4387931208","https://openalex.org/W4387951124","https://openalex.org/W4388520896","https://openalex.org/W4388946853","https://openalex.org/W4400309819","https://openalex.org/W6605100834","https://openalex.org/W6629424454"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W1979597421","https://openalex.org/W2007980826","https://openalex.org/W2061531152","https://openalex.org/W3002753104","https://openalex.org/W2077600819","https://openalex.org/W2142036596","https://openalex.org/W2072657027","https://openalex.org/W2962838298","https://openalex.org/W2600246793"],"abstract_inverted_index":{"A":[0],"scoring":[1,40,68],"function":[2],"that":[3,77],"can":[4],"reliably":[5],"assess":[6],"the":[7,16,92],"accuracy":[8,93],"of":[9,18,94],"a":[10,61,104],"3D":[11,70],"RNA":[12,39,69],"structural":[13,113],"model":[14,26],"in":[15,103],"absence":[17],"experimental":[19],"structure":[20],"is":[21,144],"not":[22],"only":[23],"important":[24],"for":[25,33,67],"evaluation":[27],"and":[28,51,97,130,132,137],"selection":[29],"but":[30],"also":[31],"useful":[32],"scoring-guided":[34],"conformational":[35],"sampling.":[36],"However,":[37],"high-fidelity":[38],"has":[41],"proven":[42],"to":[43,110],"be":[44],"difficult":[45],"using":[46],"conventional":[47],"knowledge-based":[48],"statistical":[49,125],"potentials":[50,126],"currently":[52],"available":[53,146],"machine":[54,74,133],"learning-based":[55],"approaches.":[56],"Here,":[57],"we":[58],"present":[59],"lociPARSE,":[60],"locality-aware":[62],"invariant":[63],"point":[64],"attention":[65],"architecture":[66],"structures.":[71],"Unlike":[72],"existing":[73,124],"learning":[75,134],"methods":[76,135],"estimate":[78],"superposition-based":[79],"root-mean-square":[80],"deviation":[81],"(RMSD),":[82],"lociPARSE":[83,121,143],"estimates":[84],"Local":[85],"Distance":[86],"Difference":[87],"Test":[88],"(lDDT)":[89],"scores":[90],"capturing":[91],"each":[95],"nucleotide":[96],"its":[98],"surrounding":[99],"local":[100],"atomic":[101],"environment":[102],"superposition-free":[105],"manner,":[106],"before":[107],"aggregating":[108],"information":[109],"predict":[111],"global":[112],"accuracy.":[114],"Tested":[115],"on":[116],"multiple":[117],"datasets":[118],"including":[119],"CASP15,":[120],"significantly":[122],"outperforms":[123],"(rsRNASP,":[127],"cgRNASP,":[128],"DFIRE-RNA,":[129],"RASP)":[131],"(ARES":[136],"RNA3DCNN)":[138],"across":[139],"complementary":[140],"assessment":[141],"metrics.":[142],"freely":[145],"at":[147],"https://github.com/Bhattacharya-Lab/lociPARSE.":[148]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":7}],"updated_date":"2026-06-25T08:15:23.626066","created_date":"2025-10-10T00:00:00"}
