{"id":"https://openalex.org/W4317242647","doi":"https://doi.org/10.1371/journal.pcbi.1010851","title":"End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins","display_name":"End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins","publication_year":2023,"publication_date":"2023-01-18","ids":{"openalex":"https://openalex.org/W4317242647","doi":"https://doi.org/10.1371/journal.pcbi.1010851","pmid":"https://pubmed.ncbi.nlm.nih.gov/36652496"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1010851","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010851","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010851&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010851&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043728103","display_name":"Tian Cai","orcid":"https://orcid.org/0000-0002-9516-6489"},"institutions":[{"id":"https://openalex.org/I121847817","display_name":"The Graduate Center, CUNY","ror":"https://ror.org/00awd9g61","country_code":"US","type":"education","lineage":["https://openalex.org/I121847817"]},{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tian Cai","raw_affiliation_strings":["Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, New York, United States of America","institution_ids":["https://openalex.org/I174216632","https://openalex.org/I121847817"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051041953","display_name":"Li Xie","orcid":"https://orcid.org/0000-0003-3658-2535"},"institutions":[{"id":"https://openalex.org/I121847817","display_name":"The Graduate Center, CUNY","ror":"https://ror.org/00awd9g61","country_code":"US","type":"education","lineage":["https://openalex.org/I121847817"]},{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]},{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I39694355","display_name":"Hunter College","ror":"https://ror.org/00g2xk477","country_code":"US","type":"education","lineage":["https://openalex.org/I39694355"]},{"id":"https://openalex.org/I4210097825","display_name":"MIND Research Institute","ror":"https://ror.org/00we1gw23","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210097825"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Li Xie","raw_affiliation_strings":["Department of Computer Science, Hunter College, The City University of New York, New York, New York, United States of America","Helen and Robert Appel Alzheimer's Disease Research Institute, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, New York, United States of America","Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hunter College, The City University of New York, New York, New York, United States of America","institution_ids":["https://openalex.org/I39694355","https://openalex.org/I174216632"]},{"raw_affiliation_string":"Helen and Robert Appel Alzheimer's Disease Research Institute, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, New York, United States of America","institution_ids":["https://openalex.org/I4210097825","https://openalex.org/I205783295"]},{"raw_affiliation_string":"Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, New York, United States of America","institution_ids":["https://openalex.org/I174216632","https://openalex.org/I121847817"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100450352","display_name":"Shuo Zhang","orcid":"https://orcid.org/0000-0001-9497-6263"},"institutions":[{"id":"https://openalex.org/I121847817","display_name":"The Graduate Center, CUNY","ror":"https://ror.org/00awd9g61","country_code":"US","type":"education","lineage":["https://openalex.org/I121847817"]},{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Shuo Zhang","raw_affiliation_strings":["Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, New York, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-9497-6263","affiliations":[{"raw_affiliation_string":"Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, New York, United States of America","institution_ids":["https://openalex.org/I174216632","https://openalex.org/I121847817"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072162844","display_name":"Muge Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I36672615","display_name":"Courant Institute of Mathematical Sciences","ror":"https://ror.org/037tm7f56","country_code":"US","type":"education","lineage":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Muge Chen","raw_affiliation_strings":["Master Program in Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Master Program in Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, New York, United States of America","institution_ids":["https://openalex.org/I36672615","https://openalex.org/I57206974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100739031","display_name":"Di He","orcid":"https://orcid.org/0000-0002-0908-9123"},"institutions":[{"id":"https://openalex.org/I121847817","display_name":"The Graduate Center, CUNY","ror":"https://ror.org/00awd9g61","country_code":"US","type":"education","lineage":["https://openalex.org/I121847817"]},{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Di He","raw_affiliation_strings":["Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, New York, United States of America","institution_ids":["https://openalex.org/I174216632","https://openalex.org/I121847817"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066226479","display_name":"Amitesh Badkul","orcid":"https://orcid.org/0009-0000-9207-1954"},"institutions":[{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]},{"id":"https://openalex.org/I39694355","display_name":"Hunter College","ror":"https://ror.org/00g2xk477","country_code":"US","type":"education","lineage":["https://openalex.org/I39694355"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Amitesh Badkul","raw_affiliation_strings":["Department of Computer Science, Hunter College, The City University of New York, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hunter College, The City University of New York, New York, New York, United States of America","institution_ids":["https://openalex.org/I39694355","https://openalex.org/I174216632"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100355987","display_name":"Yang Liu","orcid":"https://orcid.org/0000-0002-8064-7108"},"institutions":[{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]},{"id":"https://openalex.org/I39694355","display_name":"Hunter College","ror":"https://ror.org/00g2xk477","country_code":"US","type":"education","lineage":["https://openalex.org/I39694355"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yang Liu","raw_affiliation_strings":["Department of Computer Science, Hunter College, The City University of New York, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hunter College, The City University of New York, New York, New York, United States of America","institution_ids":["https://openalex.org/I39694355","https://openalex.org/I174216632"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071878570","display_name":"Hari Krishna Namballa","orcid":null},"institutions":[{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]},{"id":"https://openalex.org/I39694355","display_name":"Hunter College","ror":"https://ror.org/00g2xk477","country_code":"US","type":"education","lineage":["https://openalex.org/I39694355"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hari Krishna Namballa","raw_affiliation_strings":["Department of Chemistry, Hunter College, The City University of New York, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Hunter College, The City University of New York, New York, New York, United States of America","institution_ids":["https://openalex.org/I39694355","https://openalex.org/I174216632"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088331367","display_name":"Michael Dorogan","orcid":"https://orcid.org/0000-0001-9431-2539"},"institutions":[{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]},{"id":"https://openalex.org/I39694355","display_name":"Hunter College","ror":"https://ror.org/00g2xk477","country_code":"US","type":"education","lineage":["https://openalex.org/I39694355"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michael Dorogan","raw_affiliation_strings":["Department of Chemistry, Hunter College, The City University of New York, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Hunter College, The City University of New York, New York, New York, United States of America","institution_ids":["https://openalex.org/I39694355","https://openalex.org/I174216632"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070480197","display_name":"Wayne W. Harding","orcid":"https://orcid.org/0000-0002-1866-3553"},"institutions":[{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]},{"id":"https://openalex.org/I39694355","display_name":"Hunter College","ror":"https://ror.org/00g2xk477","country_code":"US","type":"education","lineage":["https://openalex.org/I39694355"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Wayne W. Harding","raw_affiliation_strings":["Department of Chemistry, Hunter College, The City University of New York, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Hunter College, The City University of New York, New York, New York, United States of America","institution_ids":["https://openalex.org/I39694355","https://openalex.org/I174216632"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022761529","display_name":"Cameron Mura","orcid":"https://orcid.org/0000-0001-7985-2561"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Cameron Mura","raw_affiliation_strings":["School of Data Science & Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-7985-2561","affiliations":[{"raw_affiliation_string":"School of Data Science & Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075833022","display_name":"Philip E. Bourne","orcid":"https://orcid.org/0000-0002-7618-7292"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Philip E. Bourne","raw_affiliation_strings":["School of Data Science & Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Data Science & Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066245750","display_name":"Lei Xie","orcid":"https://orcid.org/0000-0001-9051-2111"},"institutions":[{"id":"https://openalex.org/I121847817","display_name":"The Graduate Center, CUNY","ror":"https://ror.org/00awd9g61","country_code":"US","type":"education","lineage":["https://openalex.org/I121847817"]},{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]},{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I39694355","display_name":"Hunter College","ror":"https://ror.org/00g2xk477","country_code":"US","type":"education","lineage":["https://openalex.org/I39694355"]},{"id":"https://openalex.org/I4210097825","display_name":"MIND Research Institute","ror":"https://ror.org/00we1gw23","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210097825"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lei Xie","raw_affiliation_strings":["Department of Computer Science, Hunter College, The City University of New York, New York, New York, United States of America","Helen and Robert Appel Alzheimer's Disease Research Institute, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, New York, United States of America","Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, New York, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-9051-2111","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hunter College, The City University of New York, New York, New York, United States of America","institution_ids":["https://openalex.org/I39694355","https://openalex.org/I174216632"]},{"raw_affiliation_string":"Helen and Robert Appel Alzheimer's Disease Research Institute, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, New York, United States of America","institution_ids":["https://openalex.org/I4210097825","https://openalex.org/I205783295"]},{"raw_affiliation_string":"Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, New York, United States of America","institution_ids":["https://openalex.org/I174216632","https://openalex.org/I121847817"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":13,"corresponding_author_ids":["https://openalex.org/A5022761529","https://openalex.org/A5043728103","https://openalex.org/A5051041953","https://openalex.org/A5066226479","https://openalex.org/A5066245750","https://openalex.org/A5070480197","https://openalex.org/A5071878570","https://openalex.org/A5072162844","https://openalex.org/A5075833022","https://openalex.org/A5088331367","https://openalex.org/A5100355987","https://openalex.org/A5100450352","https://openalex.org/A5100739031"],"corresponding_institution_ids":["https://openalex.org/I121847817","https://openalex.org/I174216632","https://openalex.org/I205783295","https://openalex.org/I36672615","https://openalex.org/I39694355","https://openalex.org/I4210097825","https://openalex.org/I51556381","https://openalex.org/I57206974"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":4.0559,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.94800173,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"19","issue":"1","first_page":"e1010851","last_page":"e1010851"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9994999766349792,"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":0.9994999766349792,"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/T10044","display_name":"Protein Structure and Dynamics","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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9965000152587891,"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/computational-biology","display_name":"Computational biology","score":0.6157615780830383},{"id":"https://openalex.org/keywords/protein-function-prediction","display_name":"Protein function prediction","score":0.5141025185585022},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.501497745513916},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.45979711413383484},{"id":"https://openalex.org/keywords/functional-genomics","display_name":"Functional genomics","score":0.4507664144039154},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4495212435722351},{"id":"https://openalex.org/keywords/protein-ligand","display_name":"Protein ligand","score":0.4413134455680847},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.44098877906799316},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.423639178276062},{"id":"https://openalex.org/keywords/human-genome","display_name":"Human genome","score":0.4224597215652466},{"id":"https://openalex.org/keywords/protein-family","display_name":"Protein family","score":0.41585808992385864},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4024042785167694},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3958350419998169},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.37874671816825867},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3545430898666382},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2901070713996887},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.23439225554466248}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6157615780830383},{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.5141025185585022},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.501497745513916},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.45979711413383484},{"id":"https://openalex.org/C161078062","wikidata":"https://www.wikidata.org/wiki/Q1068690","display_name":"Functional genomics","level":5,"score":0.4507664144039154},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4495212435722351},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.4413134455680847},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.44098877906799316},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.423639178276062},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.4224597215652466},{"id":"https://openalex.org/C171897839","wikidata":"https://www.wikidata.org/wiki/Q417841","display_name":"Protein family","level":3,"score":0.41585808992385864},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4024042785167694},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3958350419998169},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.37874671816825867},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3545430898666382},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2901070713996887},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.23439225554466248},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","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":"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1010851","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010851","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010851&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:36652496","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36652496","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9886305","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9886305","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9886305/pdf/pcbi.1010851.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":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:9ff4f70275c349c3ab853db6901603ee","is_oa":true,"landing_page_url":"https://doaj.org/article/9ff4f70275c349c3ab853db6901603ee","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 19, Iss 1, p e1010851 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1010851","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010851","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010851&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.4399999976158142,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G2980691641","display_name":null,"funder_award_id":"R01AD057555","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G4761146192","display_name":null,"funder_award_id":"HHSN-271-2008-00025-C","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G5104326092","display_name":null,"funder_award_id":"2226183","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6392594831","display_name":null,"funder_award_id":"R01GM122845","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332600","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33"},{"id":"https://openalex.org/F4320337337","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11"},{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4317242647.pdf","grobid_xml":"https://content.openalex.org/works/W4317242647.grobid-xml"},"referenced_works_count":59,"referenced_works":["https://openalex.org/W785925703","https://openalex.org/W1968319881","https://openalex.org/W2000864931","https://openalex.org/W2015147525","https://openalex.org/W2016464448","https://openalex.org/W2018661561","https://openalex.org/W2066244040","https://openalex.org/W2092285329","https://openalex.org/W2130479394","https://openalex.org/W2134967712","https://openalex.org/W2150782426","https://openalex.org/W2169815691","https://openalex.org/W2194775991","https://openalex.org/W2336341683","https://openalex.org/W2464732678","https://openalex.org/W2511656322","https://openalex.org/W2558999090","https://openalex.org/W2562883249","https://openalex.org/W2604527271","https://openalex.org/W2604763608","https://openalex.org/W2785947426","https://openalex.org/W2794241347","https://openalex.org/W2802492120","https://openalex.org/W2809216727","https://openalex.org/W2893697380","https://openalex.org/W2918063357","https://openalex.org/W2951276412","https://openalex.org/W2953799871","https://openalex.org/W2983166786","https://openalex.org/W3000043291","https://openalex.org/W3011342203","https://openalex.org/W3094762523","https://openalex.org/W3095583226","https://openalex.org/W3123462448","https://openalex.org/W3124481204","https://openalex.org/W3126039337","https://openalex.org/W3132153121","https://openalex.org/W3135588948","https://openalex.org/W3137581839","https://openalex.org/W3146944767","https://openalex.org/W3162362563","https://openalex.org/W3163842339","https://openalex.org/W3167575787","https://openalex.org/W3167852095","https://openalex.org/W3170208818","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3199468887","https://openalex.org/W3201866154","https://openalex.org/W4224126566","https://openalex.org/W4225277682","https://openalex.org/W4229449348","https://openalex.org/W4229452091","https://openalex.org/W4250772482","https://openalex.org/W4300861364","https://openalex.org/W4306412305","https://openalex.org/W6703335439","https://openalex.org/W6772452955","https://openalex.org/W6776331362"],"related_works":["https://openalex.org/W2119410807","https://openalex.org/W3207928532","https://openalex.org/W2108768153","https://openalex.org/W2125494000","https://openalex.org/W1914481269","https://openalex.org/W2003165115","https://openalex.org/W2800194647","https://openalex.org/W1568915309","https://openalex.org/W3035561473","https://openalex.org/W2169356867"],"abstract_inverted_index":{"Systematically":[0],"discovering":[1],"protein-ligand":[2,199],"interactions":[3],"across":[4,98],"the":[5,52,92,108,120,145,164,170,228,232,237,276,300,309,335],"entire":[6],"human":[7,311],"and":[8,21,131,143,152,172,186,198,207,215,307,322],"pathogen":[9],"genomes":[10],"is":[11,330],"critical":[12],"in":[13,163,169,180,223,290,338],"chemical":[14],"genomics,":[15],"protein":[16,54,255,271,343],"function":[17,116],"prediction,":[18],"drug":[19,291],"discovery,":[20],"many":[22],"other":[23],"areas.":[24],"However,":[25],"more":[26],"than":[27],"90%":[28],"of":[29,76,110,112,138,195,234,296,302,342],"gene":[30,99,140,150,161,205],"families":[31,141,162],"remain":[32],"\"dark\"-i.e.,":[33],"their":[34],"small-molecule":[35],"ligands":[36,137],"are":[37],"undiscovered":[38],"due":[39],"to":[40,90,106,147,176,203,266,282,286,334],"experimental":[41],"limitations":[42],"or":[43],"human/historical":[44],"biases.":[45],"Existing":[46],"computational":[47],"approaches":[48],"typically":[49],"fail":[50],"when":[51,201],"dark":[53,149,204],"differs":[55],"from":[56,135,167,240],"those":[57,168],"with":[58],"known":[59],"ligands.":[60],"To":[61],"address":[62],"this":[63],"challenge,":[64],"we":[65],"have":[66,320],"developed":[67],"a":[68,81,124,148,154,181,248,331],"deep":[69,251],"learning":[70,197,252],"framework,":[71,253],"called":[72],"PortalCG,":[73],"which":[74],"consists":[75],"four":[77],"novel":[78],"components:":[79],"(i)":[80],"3-dimensional":[82],"ligand":[83],"binding":[84],"site":[85],"enhanced":[86],"sequence":[87],"pre-training":[88],"strategy":[89,105],"encode":[91],"evolutionary":[93],"links":[94],"between":[95],"ligand-binding":[96],"sites":[97],"families;":[100],"(ii)":[101],"an":[102,224,260],"end-to-end":[103],"pretraining-fine-tuning":[104],"reduce":[107],"impact":[109],"inaccuracy":[111],"predicted":[113,270],"structures":[114,272],"on":[115],"predictions":[117],"by":[118],"recognizing":[119],"sequence-structure-function":[121,250],"paradigm;":[122],"(iii)":[123],"new":[125],"out-of-cluster":[126],"meta-learning":[127],"algorithm":[128],"that":[129,247,316,328],"extracts":[130],"accumulates":[132],"information":[133,257],"learned":[134],"predicting":[136],"distinct":[139],"(meta-data)":[142],"applies":[144],"meta-data":[146],"family;":[151],"(iv)":[153],"stress":[155],"model":[156,178],"selection":[157],"step,":[158],"using":[159],"different":[160],"test":[165],"data":[166,174],"training":[171],"development":[173],"sets":[175],"facilitate":[177],"deployment":[179],"real-world":[182],"scenario.":[183],"In":[184],"extensive":[185],"rigorous":[187],"benchmark":[188],"experiments,":[189],"PortalCG":[190,235,281,329],"considerably":[191],"outperformed":[192],"state-of-the-art":[193],"techniques":[194],"machine":[196],"docking":[200],"applied":[202,280],"families,":[206],"demonstrated":[208],"its":[209,288],"generalization":[210],"power":[211],"for":[212,227,275,299,313],"target":[213,314],"identifications":[214],"compound":[216,230,277],"screenings":[217],"under":[218],"out-of-distribution":[219],"(OOD)":[220],"scenarios.":[221],"Furthermore,":[222],"external":[225],"validation":[226],"multi-target":[229],"screening,":[231],"performance":[233],"surpassed":[236],"rational":[238],"design":[239],"medicinal":[241],"chemists.":[242],"Our":[243,325],"results":[244,326],"also":[245],"suggest":[246],"differentiable":[249],"where":[254,269],"structural":[256],"serves":[258],"as":[259],"intermediate":[261],"layer,":[262],"could":[263],"be":[264],"superior":[265],"conventional":[267],"methodology":[268],"were":[273],"used":[274],"screening.":[278],"We":[279],"two":[283],"case":[284],"studies":[285],"exemplify":[287],"potential":[289],"discovery:":[292],"designing":[293],"selective":[294],"dual-antagonists":[295],"dopamine":[297],"receptors":[298],"treatment":[301],"opioid":[303],"use":[304],"disorder":[305],"(OUD),":[306],"illuminating":[308],"understudied":[310,340],"genome":[312],"diseases":[315],"do":[317],"not":[318],"yet":[319],"effective":[321],"safe":[323],"therapeutics.":[324],"suggested":[327],"viable":[332],"solution":[333],"OOD":[336],"problem":[337],"exploring":[339],"regions":[341],"functional":[344],"space.":[345]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":4}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}