{"id":"https://openalex.org/W4406530061","doi":"https://doi.org/10.1021/acs.jcim.4c01765","title":"NesT-NABind: a Nested Transformer for Nucleic Acid-Binding Site Prediction on Protein Surface","display_name":"NesT-NABind: a Nested Transformer for Nucleic Acid-Binding Site Prediction on Protein Surface","publication_year":2025,"publication_date":"2025-01-17","ids":{"openalex":"https://openalex.org/W4406530061","doi":"https://doi.org/10.1021/acs.jcim.4c01765","pmid":"https://pubmed.ncbi.nlm.nih.gov/39818834"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c01765","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01765","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100732413","display_name":"Xinyue Ma","orcid":"https://orcid.org/0009-0001-9577-5583"},"institutions":[{"id":"https://openalex.org/I30809798","display_name":"ShanghaiTech University","ror":"https://ror.org/030bhh786","country_code":"CN","type":"education","lineage":["https://openalex.org/I30809798"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xinyue Ma","raw_affiliation_strings":["School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New Area, Shanghai 201210, China","Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New Area, Shanghai 201210, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New Area, Shanghai 201210, China","institution_ids":["https://openalex.org/I30809798"]},{"raw_affiliation_string":"Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New Area, Shanghai 201210, China","institution_ids":["https://openalex.org/I30809798"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102021687","display_name":"Fenglei Li","orcid":"https://orcid.org/0009-0006-2145-1347"},"institutions":[{"id":"https://openalex.org/I30809798","display_name":"ShanghaiTech University","ror":"https://ror.org/030bhh786","country_code":"CN","type":"education","lineage":["https://openalex.org/I30809798"]},{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["CN","FI"],"is_corresponding":false,"raw_author_name":"Fenglei Li","raw_affiliation_strings":["Department of Computer Science, Aalto University,Konemiehentie 2, Espoo02150,Finland","School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New Area, Shanghai 201210, China","Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New Area, Shanghai 201210, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Aalto University,Konemiehentie 2, Espoo02150,Finland","institution_ids":["https://openalex.org/I9927081"]},{"raw_affiliation_string":"School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New Area, Shanghai 201210, China","institution_ids":["https://openalex.org/I30809798"]},{"raw_affiliation_string":"Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New Area, Shanghai 201210, China","institution_ids":["https://openalex.org/I30809798"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015681671","display_name":"Qianyu Chen","orcid":"https://orcid.org/0000-0002-1273-7988"},"institutions":[{"id":"https://openalex.org/I30809798","display_name":"ShanghaiTech University","ror":"https://ror.org/030bhh786","country_code":"CN","type":"education","lineage":["https://openalex.org/I30809798"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qianyu Chen","raw_affiliation_strings":["School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New Area, Shanghai 201210, China","Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New Area, Shanghai 201210, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New Area, Shanghai 201210, China","institution_ids":["https://openalex.org/I30809798"]},{"raw_affiliation_string":"Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New Area, Shanghai 201210, China","institution_ids":["https://openalex.org/I30809798"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Shenghua Gao","orcid":null},"institutions":[{"id":"https://openalex.org/I200769079","display_name":"Hong Kong University of Science and Technology","ror":"https://ror.org/00q4vv597","country_code":"HK","type":"education","lineage":["https://openalex.org/I200769079"]},{"id":"https://openalex.org/I4210151021","display_name":"Shanghai Institute of Computing Technology","ror":"https://ror.org/05ek0ze18","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210151021"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["CN","HK"],"is_corresponding":true,"raw_author_name":"Shenghua Gao","raw_affiliation_strings":["Department of Computer Science, The University of Hong Kong, Pokfolam Road, HKSAR, 999077, China","HKU Shanghai lntelligent Computing Research Center","HKU Shanghai lntelligent Computing Research Center, Shanghai, 201210, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, The University of Hong Kong, Pokfolam Road, HKSAR, 999077, China","institution_ids":["https://openalex.org/I200769079","https://openalex.org/I889458895"]},{"raw_affiliation_string":"HKU Shanghai lntelligent Computing Research Center","institution_ids":["https://openalex.org/I4210151021","https://openalex.org/I889458895"]},{"raw_affiliation_string":"HKU Shanghai lntelligent Computing Research Center, Shanghai, 201210, China","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068731692","display_name":"Fang Bai","orcid":"https://orcid.org/0000-0003-1468-5568"},"institutions":[{"id":"https://openalex.org/I30809798","display_name":"ShanghaiTech University","ror":"https://ror.org/030bhh786","country_code":"CN","type":"education","lineage":["https://openalex.org/I30809798"]},{"id":"https://openalex.org/I4210157781","display_name":"Shanghai Clinical Research Center","ror":"https://ror.org/057tkkm33","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210157781"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Fang Bai","raw_affiliation_strings":["School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New Area, Shanghai 201210, China","School of Life Science and Technology, ShanghaiTech University, Pudong New Area, 393 Middle Huaxia Road, Shanghai 201210, China","Shanghai Clinical Research and Trial Center, No.1599 Keyuan Road, Pudong New Area, Shanghai 201210, China","Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New Area, Shanghai 201210, China"],"raw_orcid":"https://orcid.org/0000-0003-1468-5568","affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New Area, Shanghai 201210, China","institution_ids":["https://openalex.org/I30809798"]},{"raw_affiliation_string":"School of Life Science and Technology, ShanghaiTech University, Pudong New Area, 393 Middle Huaxia Road, Shanghai 201210, China","institution_ids":["https://openalex.org/I30809798"]},{"raw_affiliation_string":"Shanghai Clinical Research and Trial Center, No.1599 Keyuan Road, Pudong New Area, Shanghai 201210, China","institution_ids":["https://openalex.org/I4210157781"]},{"raw_affiliation_string":"Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New Area, Shanghai 201210, China","institution_ids":["https://openalex.org/I30809798"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5068731692"],"corresponding_institution_ids":["https://openalex.org/I200769079","https://openalex.org/I30809798","https://openalex.org/I4210151021","https://openalex.org/I4210157781","https://openalex.org/I889458895"],"apc_list":null,"apc_paid":null,"fwci":2.567,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.88501385,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"65","issue":"3","first_page":"1166","last_page":"1177"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9994999766349792,"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":0.9994999766349792,"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":0.9994000196456909,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9991000294685364,"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/nucleic-acid","display_name":"Nucleic acid","score":0.5327848196029663},{"id":"https://openalex.org/keywords/surface-protein","display_name":"Surface protein","score":0.4516925811767578},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.43802890181541443},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3999185264110565},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37460052967071533},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3620292544364929},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3435029983520508},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2821195125579834},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1966792643070221},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.0911073088645935},{"id":"https://openalex.org/keywords/electrical-engineering","display_name":"Electrical engineering","score":0.08937683701515198}],"concepts":[{"id":"https://openalex.org/C24107716","wikidata":"https://www.wikidata.org/wiki/Q123619","display_name":"Nucleic acid","level":2,"score":0.5327848196029663},{"id":"https://openalex.org/C3019232848","wikidata":"https://www.wikidata.org/wiki/Q29548","display_name":"Surface protein","level":2,"score":0.4516925811767578},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.43802890181541443},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3999185264110565},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37460052967071533},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3620292544364929},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3435029983520508},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2821195125579834},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1966792643070221},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.0911073088645935},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.08937683701515198},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":false},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.4c01765","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01765","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:39818834","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39818834","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:hub.hku.hk:10722/358587","is_oa":false,"landing_page_url":"https://hub.hku.hk/handle/10722/358587","pdf_url":null,"source":{"id":"https://openalex.org/S4377196271","display_name":"The HKU Scholars Hub (University of Hong Kong)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I889458895","host_organization_name":"University of Hong Kong","host_organization_lineage":["https://openalex.org/I889458895"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1042291103","display_name":null,"funder_award_id":"2022YFC3400500","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G1975032899","display_name":null,"funder_award_id":"24YF2729200","funder_id":"https://openalex.org/F4320313610","funder_display_name":"Shanghai Science and Technology Development Foundation"},{"id":"https://openalex.org/G5524584715","display_name":null,"funder_award_id":"2022YFC3400501","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G6145034552","display_name":null,"funder_award_id":"24JS2850100","funder_id":"https://openalex.org/F4320313610","funder_display_name":"Shanghai Science and Technology Development Foundation"},{"id":"https://openalex.org/G838114600","display_name":null,"funder_award_id":"24JS2850200","funder_id":"https://openalex.org/F4320313610","funder_display_name":"Shanghai Science and Technology Development Foundation"}],"funders":[{"id":"https://openalex.org/F4320313610","display_name":"Shanghai Science and Technology Development Foundation","ror":null},{"id":"https://openalex.org/F4320327675","display_name":"ShanghaiTech University","ror":"https://ror.org/030bhh786"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W1931339766","https://openalex.org/W1985398661","https://openalex.org/W1997535872","https://openalex.org/W2015159529","https://openalex.org/W2018661561","https://openalex.org/W2031168104","https://openalex.org/W2102245393","https://openalex.org/W2102461176","https://openalex.org/W2115339329","https://openalex.org/W2156125289","https://openalex.org/W2165558283","https://openalex.org/W2170747616","https://openalex.org/W2501193935","https://openalex.org/W2582176104","https://openalex.org/W2807540482","https://openalex.org/W2892720054","https://openalex.org/W2940734441","https://openalex.org/W2949650786","https://openalex.org/W2979750740","https://openalex.org/W2990138404","https://openalex.org/W2992752586","https://openalex.org/W3014677172","https://openalex.org/W3043489078","https://openalex.org/W3094502228","https://openalex.org/W3116323439","https://openalex.org/W3146944767","https://openalex.org/W4205617467","https://openalex.org/W4206911836","https://openalex.org/W4210262283","https://openalex.org/W4214708455","https://openalex.org/W4286500588","https://openalex.org/W4290672950","https://openalex.org/W4293003482","https://openalex.org/W4364381349","https://openalex.org/W4366239108","https://openalex.org/W4367396488","https://openalex.org/W4382937503","https://openalex.org/W4385245566","https://openalex.org/W4385407166","https://openalex.org/W4386303561","https://openalex.org/W4388946853","https://openalex.org/W4389126617","https://openalex.org/W4392011513","https://openalex.org/W4394652702","https://openalex.org/W4394666973","https://openalex.org/W4396721167","https://openalex.org/W4399564102","https://openalex.org/W4400231442","https://openalex.org/W4400926341"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W1837502840"],"abstract_inverted_index":{"Protein\u2013nucleic":[0],"acid":[1],"interactions":[2],"play":[3],"a":[4,87,118,130,162,170,202],"crucial":[5],"role":[6],"in":[7,108,165,173,201],"many":[8],"physiological":[9],"processes.":[10],"Identifying":[11],"the":[12,18,22,26,31,39,70,76,104,141,154,166,180,192],"binding":[13],"sites":[14,49,74],"of":[15,34,151,182,206],"nucleotides":[16],"on":[17,62,140],"protein":[19,78],"surface":[20,124,136],"is":[21],"prerequisite":[23],"for":[24,92,191],"understanding":[25,110],"molecular":[27],"recognition":[28],"mechanisms":[29],"between":[30],"two":[32,145],"types":[33],"macromolecules":[35],"and":[36,75,111,129,137,169,196],"also":[37],"provides":[38],"information":[40,125,139],"to":[41,50,55,122,134,176],"design":[42],"or":[43],"generate":[44],"molecule":[45],"modulators":[46],"against":[47],"these":[48,73],"manipulate":[51],"biological":[52],"function":[53],"according":[54],"specific":[56],"requirements.":[57],"Existing":[58],"studies":[59],"mainly":[60],"focus":[61],"characterizing":[63],"local":[64,119],"surfaces":[65],"around":[66,126],"sites,":[67],"often":[68],"neglecting":[69],"interrelationships":[71],"among":[72],"global":[77,131,183],"information.":[79],"To":[80],"address":[81],"this":[82],"gap,":[83],"we":[84,116],"propose":[85],"NesT-NABind,":[86],"Nes":[88],"ted":[89],"T":[90],"ransformer":[91],"N":[93],"ucleic":[94],"A":[95],"cid-":[96],"Bind":[97],"ing":[98],"site":[99,128],"prediction.":[100],"This":[101],"model":[102],"leverages":[103],"Transformer\u2019s":[105],"advanced":[106],"capabilities":[107],"contextual":[109],"long-range":[112],"dependency":[113],"capturing.":[114],"Specifically,":[115],"introduce":[117],"patch-scale":[120],"Transformer":[121],"process":[123],"each":[127],"protein-scale":[132],"transformer":[133],"integrate":[135],"sequence":[138],"entire":[142],"protein.":[143],"These":[144],"Transformers":[146],"operate":[147],"at":[148],"different":[149],"scales":[150],"protein,":[152],"hence":[153],"term":[155],"\u201cnested\u201d.":[156],"Experiments":[157],"demonstrate":[158],"that":[159],"NesT-NABind":[160,185],"achieves":[161],"5.57%":[163],"improvement":[164,172],"F1":[167],"score":[168],"3.64%":[171],"AUPRC":[174],"compared":[175],"state-of-the-art":[177],"methods.":[178],"With":[179],"incorporation":[181],"features,":[184],"shows":[186],"an":[187],"enhanced":[188],"predictive":[189],"capability":[190],"challenging":[193],"large":[194],"proteins":[195],"therefore":[197],"can":[198],"be":[199],"used":[200],"much":[203],"wider":[204],"range":[205],"applications.":[207]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":2}],"updated_date":"2026-07-20T07:56:41.581041","created_date":"2025-10-10T00:00:00"}