{"id":"https://openalex.org/W4410079962","doi":"https://doi.org/10.1186/s13321-025-01023-2","title":"Application of 3D atom pair map in an attention model for enhanced drug virtual screening","display_name":"Application of 3D atom pair map in an attention model for enhanced drug virtual screening","publication_year":2025,"publication_date":"2025-05-05","ids":{"openalex":"https://openalex.org/W4410079962","doi":"https://doi.org/10.1186/s13321-025-01023-2","pmid":"https://pubmed.ncbi.nlm.nih.gov/40325489"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-01023-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01023-2","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01023-2","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01023-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Gina Ryu","orcid":null},"institutions":[{"id":"https://openalex.org/I138925566","display_name":"Ewha Womans University","ror":"https://ror.org/053fp5c05","country_code":"KR","type":"education","lineage":["https://openalex.org/I138925566"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Gina Ryu","raw_affiliation_strings":["Department of Life Sciences, College of Natural Science, Ewha Womans University, Seoul, 03760, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Life Sciences, College of Natural Science, Ewha Womans University, Seoul, 03760, Republic of Korea","institution_ids":["https://openalex.org/I138925566"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050266680","display_name":"Wankyu Kim","orcid":"https://orcid.org/0000-0003-3181-0594"},"institutions":[{"id":"https://openalex.org/I138925566","display_name":"Ewha Womans University","ror":"https://ror.org/053fp5c05","country_code":"KR","type":"education","lineage":["https://openalex.org/I138925566"]},{"id":"https://openalex.org/I4210149548","display_name":"Komipharm International (South Korea)","ror":"https://ror.org/05qb29e48","country_code":"KR","type":"company","lineage":["https://openalex.org/I4210149548"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Wankyu Kim","raw_affiliation_strings":["Department of Life Sciences, College of Natural Science, Ewha Womans University, Seoul, 03760, Republic of Korea. wkim@ewha.ac.kr","KaiPharm, Seoul, 03759, Republic of Korea. wkim@ewha.ac.kr"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Life Sciences, College of Natural Science, Ewha Womans University, Seoul, 03760, Republic of Korea. wkim@ewha.ac.kr","institution_ids":["https://openalex.org/I138925566"]},{"raw_affiliation_string":"KaiPharm, Seoul, 03759, Republic of Korea. wkim@ewha.ac.kr","institution_ids":["https://openalex.org/I4210149548"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I138925566"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":1.3095,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.81331533,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"17","issue":"1","first_page":"70","last_page":"70"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9904999732971191,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9904999732971191,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9685999751091003,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/virtual-screening","display_name":"Virtual screening","score":0.7555832862854004},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6438007354736328},{"id":"https://openalex.org/keywords/atom","display_name":"Atom (system on chip)","score":0.5273612141609192},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.4778813421726227},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39761608839035034},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.38237589597702026},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.32083189487457275},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.23852801322937012},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.22131353616714478},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.1575842797756195},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.10460776090621948}],"concepts":[{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.7555832862854004},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6438007354736328},{"id":"https://openalex.org/C58312451","wikidata":"https://www.wikidata.org/wiki/Q4817200","display_name":"Atom (system on chip)","level":2,"score":0.5273612141609192},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.4778813421726227},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39761608839035034},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.38237589597702026},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.32083189487457275},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.23852801322937012},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.22131353616714478},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.1575842797756195},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.10460776090621948},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-025-01023-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01023-2","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01023-2","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:40325489","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40325489","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 cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:9a9824c78fbc45e5b291c74600a038be","is_oa":true,"landing_page_url":"https://doaj.org/article/9a9824c78fbc45e5b291c74600a038be","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 17, Iss 1, Pp 1-10 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:10865952","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12054049","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-025-01023-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01023-2","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01023-2","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2895194335","display_name":null,"funder_award_id":"NRF-2022R1A2C1091260","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G5922187115","display_name":null,"funder_award_id":"2021R1A6A1A10039823","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G8680734909","display_name":null,"funder_award_id":"NRF-2021R1A6A1A10039823","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G8931701004","display_name":null,"funder_award_id":"2021R1A6A1A10039823","funder_id":"https://openalex.org/F4320320671","funder_display_name":"National Research Foundation"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410079962.pdf","grobid_xml":"https://content.openalex.org/works/W4410079962.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W1988037271","https://openalex.org/W2021748110","https://openalex.org/W2031390939","https://openalex.org/W2065807927","https://openalex.org/W2091155135","https://openalex.org/W2119512897","https://openalex.org/W2134967712","https://openalex.org/W2139642094","https://openalex.org/W2155478691","https://openalex.org/W2168480393","https://openalex.org/W2169546341","https://openalex.org/W2169678694","https://openalex.org/W2204695023","https://openalex.org/W2221103459","https://openalex.org/W2583907533","https://openalex.org/W2587598315","https://openalex.org/W2592742128","https://openalex.org/W2807792492","https://openalex.org/W2860192827","https://openalex.org/W2899788782","https://openalex.org/W2905012389","https://openalex.org/W2969996838","https://openalex.org/W2999554466","https://openalex.org/W3012012790","https://openalex.org/W3047812492","https://openalex.org/W3104537585","https://openalex.org/W3104705366","https://openalex.org/W3159719254","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3201055938","https://openalex.org/W4205749506","https://openalex.org/W4206305620","https://openalex.org/W4206936290","https://openalex.org/W4207018334","https://openalex.org/W4211218744","https://openalex.org/W4285041843","https://openalex.org/W4307468223","https://openalex.org/W4365484962","https://openalex.org/W4389991855","https://openalex.org/W4405514997"],"related_works":["https://openalex.org/W3180887190","https://openalex.org/W2320211095","https://openalex.org/W2308164565","https://openalex.org/W2062768126","https://openalex.org/W3003855012","https://openalex.org/W2059230675","https://openalex.org/W2376003823","https://openalex.org/W4402273478","https://openalex.org/W2594726310","https://openalex.org/W2355193834"],"abstract_inverted_index":{"SCIENTIFIC":[0],"CONTRIBUTION:":[1],"This":[2],"study":[3],"demonstrates":[4],"the":[5],"utility":[6],"of":[7],"a":[8,15],"novel":[9],"molecular":[10],"representation,":[11],"3D":[12,42],"APM":[13,43],"and":[14],"deep":[16],"learning":[17],"model":[18],"based":[19],"on":[20],"it":[21],"for":[22],"virtual":[23],"screening,":[24],"suggesting":[25],"that":[26],"many":[27],"other":[28],"prediction":[29],"models":[30],"would":[31],"also":[32],"benefit":[33],"from":[34],"adopting":[35],"APM.":[36],"An":[37],"open-source":[38],"script":[39],"to":[40],"generate":[41],"is":[44],"available":[45],"at":[46],"https://github.com/rimeless/APM.":[47]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-28T14:05:53.105641","created_date":"2025-10-10T00:00:00"}