{"id":"https://openalex.org/W4413807593","doi":"https://doi.org/10.1186/s13321-025-01077-2","title":"Alphappimi: a comprehensive deep learning framework for predicting PPI-modulator interactions","display_name":"Alphappimi: a comprehensive deep learning framework for predicting PPI-modulator interactions","publication_year":2025,"publication_date":"2025-08-29","ids":{"openalex":"https://openalex.org/W4413807593","doi":"https://doi.org/10.1186/s13321-025-01077-2","pmid":"https://pubmed.ncbi.nlm.nih.gov/40883823"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-01077-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01077-2","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01077-2","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/s13321-025-01077-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101789308","display_name":"Dayan Liu","orcid":"https://orcid.org/0000-0001-9932-2947"},"institutions":[{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]},{"id":"https://openalex.org/I4210112270","display_name":"Qingdao Academy of Intelligent Industries","ror":"https://ror.org/02a0rnh86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210112270"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dayan Liu","raw_affiliation_strings":["College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266580, Shandong, China","Shandong Key Laboratory of Intelligent Oil & Gas Industrial Software, Qingdao, 266580, Shandong, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266580, Shandong, China","institution_ids":["https://openalex.org/I4210162190"]},{"raw_affiliation_string":"Shandong Key Laboratory of Intelligent Oil & Gas Industrial Software, Qingdao, 266580, Shandong, China","institution_ids":["https://openalex.org/I4210112270"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006420025","display_name":"Tao Song","orcid":"https://orcid.org/0000-0002-0130-3340"},"institutions":[{"id":"https://openalex.org/I4210112270","display_name":"Qingdao Academy of Intelligent Industries","ror":"https://ror.org/02a0rnh86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210112270"]},{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tao Song","raw_affiliation_strings":["College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266580, Shandong, China","Shandong Key Laboratory of Intelligent Oil & Gas Industrial Software, Qingdao, 266580, Shandong, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266580, Shandong, China","institution_ids":["https://openalex.org/I4210162190"]},{"raw_affiliation_string":"Shandong Key Laboratory of Intelligent Oil & Gas Industrial Software, Qingdao, 266580, Shandong, China","institution_ids":["https://openalex.org/I4210112270"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100375555","display_name":"Shuang Wang","orcid":"https://orcid.org/0000-0001-5933-074X"},"institutions":[{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]},{"id":"https://openalex.org/I4210112270","display_name":"Qingdao Academy of Intelligent Industries","ror":"https://ror.org/02a0rnh86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210112270"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuang Wang","raw_affiliation_strings":["College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266580, Shandong, China","College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266580, Shandong, China. wangsd@upc.edu.cn","Shandong Key Laboratory of Intelligent Oil & Gas Industrial Software, Qingdao, 266580, Shandong, China","Shandong Key Laboratory of Intelligent Oil & Gas Industrial Software, Qingdao, 266580, Shandong, China. wangsd@upc.edu.cn","State Key Laboratory of Chemical Safety, Qingdao, 266580, Shandong, China. wangsd@upc.edu.cn"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266580, Shandong, China","institution_ids":["https://openalex.org/I4210162190"]},{"raw_affiliation_string":"College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266580, Shandong, China. wangsd@upc.edu.cn","institution_ids":[]},{"raw_affiliation_string":"Shandong Key Laboratory of Intelligent Oil & Gas Industrial Software, Qingdao, 266580, Shandong, China","institution_ids":["https://openalex.org/I4210112270"]},{"raw_affiliation_string":"Shandong Key Laboratory of Intelligent Oil & Gas Industrial Software, Qingdao, 266580, Shandong, China. wangsd@upc.edu.cn","institution_ids":[]},{"raw_affiliation_string":"State Key Laboratory of Chemical Safety, Qingdao, 266580, Shandong, China. wangsd@upc.edu.cn","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029016920","display_name":"Xue Li","orcid":"https://orcid.org/0000-0002-3864-6232"},"institutions":[{"id":"https://openalex.org/I4210112270","display_name":"Qingdao Academy of Intelligent Industries","ror":"https://ror.org/02a0rnh86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210112270"]},{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xue Li","raw_affiliation_strings":["College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266580, Shandong, China","Shandong Key Laboratory of Intelligent Oil & Gas Industrial Software, Qingdao, 266580, Shandong, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266580, Shandong, China","institution_ids":["https://openalex.org/I4210162190"]},{"raw_affiliation_string":"Shandong Key Laboratory of Intelligent Oil & Gas Industrial Software, Qingdao, 266580, Shandong, China","institution_ids":["https://openalex.org/I4210112270"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028526301","display_name":"Peifu Han","orcid":"https://orcid.org/0000-0003-2818-3040"},"institutions":[{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]},{"id":"https://openalex.org/I4210112270","display_name":"Qingdao Academy of Intelligent Industries","ror":"https://ror.org/02a0rnh86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210112270"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Peifu Han","raw_affiliation_strings":["College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266580, Shandong, China","Shandong Key Laboratory of Intelligent Oil & Gas Industrial Software, Qingdao, 266580, Shandong, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266580, Shandong, China","institution_ids":["https://openalex.org/I4210162190"]},{"raw_affiliation_string":"Shandong Key Laboratory of Intelligent Oil & Gas Industrial Software, Qingdao, 266580, Shandong, China","institution_ids":["https://openalex.org/I4210112270"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100373517","display_name":"Jianmin Wang","orcid":"https://orcid.org/0000-0001-6841-7943"},"institutions":[{"id":"https://openalex.org/I193775966","display_name":"Yonsei University","ror":"https://ror.org/01wjejq96","country_code":"KR","type":"education","lineage":["https://openalex.org/I193775966"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Jianmin Wang","raw_affiliation_strings":["The Interdisciplinary Graduate Program in Integrative Biotechnology, Yonsei University, Incheon, 21983, Korea. jmwang113@hotmail.com","The Interdisciplinary Graduate Program in Integrative Biotechnology, Yonsei University, Incheon, 21983, Korea"],"affiliations":[{"raw_affiliation_string":"The Interdisciplinary Graduate Program in Integrative Biotechnology, Yonsei University, Incheon, 21983, Korea. jmwang113@hotmail.com","institution_ids":[]},{"raw_affiliation_string":"The Interdisciplinary Graduate Program in Integrative Biotechnology, Yonsei University, Incheon, 21983, Korea","institution_ids":["https://openalex.org/I193775966"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5115595287","display_name":"Shudong Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210112270","display_name":"Qingdao Academy of Intelligent Industries","ror":"https://ror.org/02a0rnh86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210112270"]},{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]},{"id":"https://openalex.org/I4210156066","display_name":"State Key Laboratory of Chemical Engineering","ror":"https://ror.org/05803vc71","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210156066"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shudong Wang","raw_affiliation_strings":["College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266580, Shandong, China","College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266580, Shandong, China. wangsd@upc.edu.cn","Shandong Key Laboratory of Intelligent Oil & Gas Industrial Software, Qingdao, 266580, Shandong, China","Shandong Key Laboratory of Intelligent Oil & Gas Industrial Software, Qingdao, 266580, Shandong, China. wangsd@upc.edu.cn","State Key Laboratory of Chemical Safety, Qingdao, 266580, Shandong, China. wangsd@upc.edu.cn","State Key Laboratory of Chemical Safety, Qingdao, 266580, Shandong, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266580, Shandong, China","institution_ids":["https://openalex.org/I4210162190"]},{"raw_affiliation_string":"College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, 266580, Shandong, China. wangsd@upc.edu.cn","institution_ids":[]},{"raw_affiliation_string":"Shandong Key Laboratory of Intelligent Oil & Gas Industrial Software, Qingdao, 266580, Shandong, China","institution_ids":["https://openalex.org/I4210112270"]},{"raw_affiliation_string":"Shandong Key Laboratory of Intelligent Oil & Gas Industrial Software, Qingdao, 266580, Shandong, China. wangsd@upc.edu.cn","institution_ids":[]},{"raw_affiliation_string":"State Key Laboratory of Chemical Safety, Qingdao, 266580, Shandong, China. wangsd@upc.edu.cn","institution_ids":[]},{"raw_affiliation_string":"State Key Laboratory of Chemical Safety, Qingdao, 266580, Shandong, China","institution_ids":["https://openalex.org/I4210156066"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5100373517","https://openalex.org/A5115595287"],"corresponding_institution_ids":["https://openalex.org/I193775966","https://openalex.org/I4210112270","https://openalex.org/I4210156066","https://openalex.org/I4210162190"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.23152772,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"17","issue":"1","first_page":"134","last_page":"134"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9986000061035156,"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":0.9986000061035156,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.987500011920929,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9858999848365784,"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/computer-science","display_name":"Computer science","score":0.7952589988708496},{"id":"https://openalex.org/keywords/generalization","display_name":"Generalization","score":0.6473692059516907},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5699629783630371},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5314119458198547},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5286778807640076},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4949457049369812},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.473102331161499},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.47199538350105286},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.43993085622787476},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4164672791957855},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09837251901626587}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7952589988708496},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.6473692059516907},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5699629783630371},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5314119458198547},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5286778807640076},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4949457049369812},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.473102331161499},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.47199538350105286},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.43993085622787476},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4164672791957855},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09837251901626587},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-025-01077-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01077-2","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01077-2","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:40883823","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40883823","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:a33bae4a698d46a384c8a26f851017a0","is_oa":true,"landing_page_url":"https://doaj.org/article/a33bae4a698d46a384c8a26f851017a0","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 1-16 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12395666","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12395666/","pdf_url":null,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-025-01077-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01077-2","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01077-2","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/G1510385427","display_name":null,"funder_award_id":"tsqn201812029","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G1905417137","display_name":null,"funder_award_id":"201907116","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G2053587495","display_name":null,"funder_award_id":"201907116","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2288618935","display_name":null,"funder_award_id":"201812029","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"},{"id":"https://openalex.org/G2937860289","display_name":null,"funder_award_id":"tsqn201812029","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"},{"id":"https://openalex.org/G2957140629","display_name":null,"funder_award_id":"tsqn201812029","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3034967355","display_name":null,"funder_award_id":"201812","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G307768753","display_name":null,"funder_award_id":"62272479","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3373644481","display_name":null,"funder_award_id":"61873280","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"},{"id":"https://openalex.org/G3466627849","display_name":null,"funder_award_id":"201907116","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"},{"id":"https://openalex.org/G3614961939","display_name":null,"funder_award_id":"61972416","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G4037723416","display_name":null,"funder_award_id":"61873280","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4765083334","display_name":null,"funder_award_id":"618732","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5131945198","display_name":null,"funder_award_id":"61873280","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G5563020673","display_name":null,"funder_award_id":"61972416","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"},{"id":"https://openalex.org/G5751207120","display_name":null,"funder_award_id":"tsqn2018","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5881903318","display_name":null,"funder_award_id":"2021YFA1000103","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G6059194225","display_name":null,"funder_award_id":"61972416","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6093738109","display_name":null,"funder_award_id":"62202498","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6683504761","display_name":null,"funder_award_id":"ZR2021QF023","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"},{"id":"https://openalex.org/G6888220817","display_name":null,"funder_award_id":"tsqn2018","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"},{"id":"https://openalex.org/G7403065677","display_name":null,"funder_award_id":"62372469","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7895523656","display_name":null,"funder_award_id":"2021YFA1000102","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G8432747589","display_name":null,"funder_award_id":"24CX04029A","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G8681466026","display_name":null,"funder_award_id":"201812","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8912315176","display_name":null,"funder_award_id":"6187328","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"},{"id":"https://openalex.org/F4320324174","display_name":"Natural Science Foundation of Shandong Province","ror":null},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413807593.pdf","grobid_xml":"https://content.openalex.org/works/W4413807593.grobid-xml"},"referenced_works_count":61,"referenced_works":["https://openalex.org/W1981737096","https://openalex.org/W1988037271","https://openalex.org/W1994803330","https://openalex.org/W1997989849","https://openalex.org/W2003516462","https://openalex.org/W2034326919","https://openalex.org/W2034549041","https://openalex.org/W2038359277","https://openalex.org/W2056169996","https://openalex.org/W2087574732","https://openalex.org/W2097933346","https://openalex.org/W2098781795","https://openalex.org/W2100323510","https://openalex.org/W2101181377","https://openalex.org/W2102461176","https://openalex.org/W2119821739","https://openalex.org/W2128247932","https://openalex.org/W2135732933","https://openalex.org/W2137801157","https://openalex.org/W2145501898","https://openalex.org/W2153838454","https://openalex.org/W2155589321","https://openalex.org/W2198320582","https://openalex.org/W2295598076","https://openalex.org/W2329592726","https://openalex.org/W2589060305","https://openalex.org/W2606696614","https://openalex.org/W2607082942","https://openalex.org/W2734356283","https://openalex.org/W2735864034","https://openalex.org/W2745208859","https://openalex.org/W2783666262","https://openalex.org/W2809890174","https://openalex.org/W2815462179","https://openalex.org/W2911964244","https://openalex.org/W2912171584","https://openalex.org/W2949342052","https://openalex.org/W2953008890","https://openalex.org/W2974325953","https://openalex.org/W2992752586","https://openalex.org/W3109916301","https://openalex.org/W3133458480","https://openalex.org/W3146944767","https://openalex.org/W3154108572","https://openalex.org/W3157554109","https://openalex.org/W3177500196","https://openalex.org/W3195161349","https://openalex.org/W3201230437","https://openalex.org/W3209421341","https://openalex.org/W3217546525","https://openalex.org/W4248107770","https://openalex.org/W4282927263","https://openalex.org/W4296293027","https://openalex.org/W4313890554","https://openalex.org/W4317470261","https://openalex.org/W4323304388","https://openalex.org/W4327550249","https://openalex.org/W4387002014","https://openalex.org/W4389225229","https://openalex.org/W4399915450","https://openalex.org/W4405639953"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W4321353415","https://openalex.org/W2745001401","https://openalex.org/W2130974462","https://openalex.org/W2028665553","https://openalex.org/W2086519370","https://openalex.org/W4246352526","https://openalex.org/W2121910908","https://openalex.org/W915438175","https://openalex.org/W4230315250"],"abstract_inverted_index":{"Protein-protein":[0],"interactions":[1,104,203],"(PPIs)":[2,204],"regulate":[3],"essential":[4],"biological":[5],"processes":[6],"through":[7],"complex":[8],"interfaces,":[9],"with":[10,15,79],"their":[11,24,206],"dysfunction":[12],"is":[13],"associated":[14],"various":[16],"diseases.":[17],"Consequently,":[18],"the":[19,217,225,256],"identification":[20],"of":[21,102,220,228,258],"PPIs":[22,39],"and":[23,40,95,122,124,136,150,205,224],"interface-targeting":[25],"modulators":[26,36,151,200],"has":[27],"emerged":[28],"as":[29,45],"a":[30,68,132,173,192,212,229,251],"critical":[31],"therapeutic":[32],"approach.":[33],"However,":[34],"discovering":[35],"that":[37,73,160],"target":[38],"PPI":[41,53,88,125,148,179,260],"interfaces":[42],"remains":[43],"challenging":[44],"traditional":[46],"structure-similarity-based":[47],"methods":[48,168],"fail":[49],"to":[50,235],"effectively":[51,143],"characterize":[52],"targets,":[54],"particularly":[55,181],"those":[56,182],"for":[57,82,176,197,216,255],"which":[58],"no":[59],"active":[60],"compounds":[61],"are":[62],"known.":[63],"Here,":[64],"we":[65,97],"present":[66],"AlphaPPIMI,":[67,191],"comprehensive":[69,99,109],"deep":[70,194],"learning":[71,195],"framework":[72,107,196],"combines":[74],"large-scale":[75],"pretrained":[76,222],"language":[77,119],"models":[78,120],"domain":[80,138],"adaptation":[81],"predicting":[83,199],"PPI-modulator":[84,103],"interactions,":[85],"specifically":[86],"targeting":[87,183,201],"interface.":[89],"To":[90],"enable":[91],"robust":[92,154],"model":[93],"development":[94],"evaluation,":[96],"constructed":[98],"benchmark":[100],"datasets":[101],"(PPIMI).":[105],"Our":[106],"integrates":[108],"molecular":[110],"features":[111],"from":[112,117],"Uni-Mol2,":[113],"protein":[114,241],"representations":[115],"derived":[116],"state-of-the-art":[118],"(ESM2":[121],"ProTrans),":[123],"structural":[126],"characteristics":[127],"encoded":[128],"by":[129],"PFeature.":[130],"Through":[131],"specialized":[133,213],"cross-attention":[134,214],"architecture":[135],"conditional":[137],"adversarial":[139],"networks":[140],"(CDAN),":[141],"AlphaPPIMI":[142,161,243],"learns":[144],"potential":[145],"associations":[146],"between":[147],"targets":[149],"while":[152],"ensuring":[153],"cross-domain":[155],"generalization.":[156],"Extensive":[157],"evaluations":[158],"indicate":[159],"achieves":[162],"consistently":[163],"improved":[164],"performance":[165,246],"over":[166],"existing":[167],"in":[169],"PPIMI":[170],"prediction,":[171],"offering":[172],"promising":[174],"approach":[175],"prioritizing":[177],"candidate":[178],"modulators,":[180],"protein-protein":[184,202],"interfaces.":[185,207],"SCIENTIFIC":[186],"CONTRIBUTION:":[187],"This":[188],"work":[189],"presents":[190],"novel":[193,226],"accurately":[198],"Its":[208],"core":[209],"contributions":[210],"include":[211],"module":[215],"synergistic":[218],"fusion":[219],"multimodal":[221],"representations,":[223],"application":[227],"Conditional":[230],"Domain":[231],"Adversarial":[232],"Network":[233],"(CDAN)":[234],"significantly":[236],"improve":[237],"generalization":[238],"across":[239],"diverse":[240],"families.":[242],"demonstrates":[244],"superior":[245],"on":[247],"curated":[248],"benchmarks,":[249],"providing":[250],"powerful":[252],"computational":[253],"tool":[254],"discovery":[257],"targeted":[259],"therapeutics.":[261]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
