{"id":"https://openalex.org/W7161810072","doi":"https://doi.org/10.1186/s13321-026-01227-0","title":"Sequence-based drug-target binding site pre-training enables cryptic pocket detection and improves binding affinity and kinetics prediction","display_name":"Sequence-based drug-target binding site pre-training enables cryptic pocket detection and improves binding affinity and kinetics prediction","publication_year":2026,"publication_date":"2026-05-20","ids":{"openalex":"https://openalex.org/W7161810072","doi":"https://doi.org/10.1186/s13321-026-01227-0","pmid":"https://pubmed.ncbi.nlm.nih.gov/42163392"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-026-01227-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-026-01227-0","pdf_url":null,"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://doi.org/10.1186/s13321-026-01227-0","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5136526675","display_name":"Shuo Zhang","orcid":null},"institutions":[{"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":"Shuo Zhang","raw_affiliation_strings":["Department of Computer Science, Hunter College, The City University of New York, New York, 10065, NY, USA. shuo.zhang@hunter.cuny.edu","Helen & Robert Appel Alzheimer's Disease Research Institute, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, 10065, NY, USA. shuo.zhang@hunter.cuny.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hunter College, The City University of New York, New York, 10065, NY, USA. shuo.zhang@hunter.cuny.edu","institution_ids":["https://openalex.org/I39694355"]},{"raw_affiliation_string":"Helen & Robert Appel Alzheimer's Disease Research Institute, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, 10065, NY, USA. shuo.zhang@hunter.cuny.edu","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I4210097825"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136517766","display_name":"Li Xie","orcid":null},"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/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]},{"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":false,"raw_author_name":"Li Xie","raw_affiliation_strings":["Department of Computer Science, Hunter College, The City University of New York, New York, 10065, NY, USA","Helen & Robert Appel Alzheimer's Disease Research Institute, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, 10065, NY, USA. le.xie@northeastern.edu","Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, 10016, NY, USA. le.xie@northeastern.edu","School of Pharmacy and Pharmaceutical Sciences & Center for Drug Discovery, Northeastern University, Boston, 02115, MA, USA. le.xie@northeastern.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hunter College, The City University of New York, New York, 10065, NY, USA","institution_ids":["https://openalex.org/I39694355"]},{"raw_affiliation_string":"Helen & Robert Appel Alzheimer's Disease Research Institute, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, 10065, NY, USA. le.xie@northeastern.edu","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I4210097825"]},{"raw_affiliation_string":"Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, 10016, NY, USA. le.xie@northeastern.edu","institution_ids":["https://openalex.org/I121847817","https://openalex.org/I174216632"]},{"raw_affiliation_string":"School of Pharmacy and Pharmaceutical Sciences & Center for Drug Discovery, Northeastern University, Boston, 02115, MA, USA. le.xie@northeastern.edu","institution_ids":["https://openalex.org/I12912129"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5143817740","display_name":"Li Xie","orcid":null},"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/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]},{"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, 10065, NY, USA","Helen & Robert Appel Alzheimer's Disease Research Institute, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, 10065, NY, USA. le.xie@northeastern.edu","Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, 10016, NY, USA. le.xie@northeastern.edu","School of Pharmacy and Pharmaceutical Sciences & Center for Drug Discovery, Northeastern University, Boston, 02115, MA, USA. le.xie@northeastern.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hunter College, The City University of New York, New York, 10065, NY, USA","institution_ids":["https://openalex.org/I39694355"]},{"raw_affiliation_string":"Helen & Robert Appel Alzheimer's Disease Research Institute, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, 10065, NY, USA. le.xie@northeastern.edu","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I4210097825"]},{"raw_affiliation_string":"Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, 10016, NY, USA. le.xie@northeastern.edu","institution_ids":["https://openalex.org/I121847817","https://openalex.org/I174216632"]},{"raw_affiliation_string":"School of Pharmacy and Pharmaceutical Sciences & Center for Drug Discovery, Northeastern University, Boston, 02115, MA, USA. le.xie@northeastern.edu","institution_ids":["https://openalex.org/I12912129"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115940452","display_name":"Daniel Tiourine","orcid":null},"institutions":[{"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":false,"raw_author_name":"Daniel Tiourine","raw_affiliation_strings":["Department of Computer Science, Hunter College, The City University of New York, New York, 10065, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hunter College, The City University of New York, New York, 10065, NY, USA","institution_ids":["https://openalex.org/I39694355"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5143765628","display_name":"Lei Xie","orcid":null},"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/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]},{"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, 10065, NY, USA","Helen & Robert Appel Alzheimer's Disease Research Institute, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, 10065, NY, USA. le.xie@northeastern.edu","Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, 10016, NY, USA. le.xie@northeastern.edu","School of Pharmacy and Pharmaceutical Sciences & Center for Drug Discovery, Northeastern University, Boston, 02115, MA, USA. le.xie@northeastern.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hunter College, The City University of New York, New York, 10065, NY, USA","institution_ids":["https://openalex.org/I39694355"]},{"raw_affiliation_string":"Helen & Robert Appel Alzheimer's Disease Research Institute, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, 10065, NY, USA. le.xie@northeastern.edu","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I4210097825"]},{"raw_affiliation_string":"Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, 10016, NY, USA. le.xie@northeastern.edu","institution_ids":["https://openalex.org/I121847817","https://openalex.org/I174216632"]},{"raw_affiliation_string":"School of Pharmacy and Pharmaceutical Sciences & Center for Drug Discovery, Northeastern University, Boston, 02115, MA, USA. le.xie@northeastern.edu","institution_ids":["https://openalex.org/I12912129"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5143765628","display_name":"Lei Xie","orcid":null},"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/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]},{"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":false,"raw_author_name":"Lei Xie","raw_affiliation_strings":["Department of Computer Science, Hunter College, The City University of New York, New York, 10065, NY, USA","Helen & Robert Appel Alzheimer's Disease Research Institute, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, 10065, NY, USA. le.xie@northeastern.edu","Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, 10016, NY, USA. le.xie@northeastern.edu","School of Pharmacy and Pharmaceutical Sciences & Center for Drug Discovery, Northeastern University, Boston, 02115, MA, USA. le.xie@northeastern.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hunter College, The City University of New York, New York, 10065, NY, USA","institution_ids":["https://openalex.org/I39694355"]},{"raw_affiliation_string":"Helen & Robert Appel Alzheimer's Disease Research Institute, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, 10065, NY, USA. le.xie@northeastern.edu","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I4210097825"]},{"raw_affiliation_string":"Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, 10016, NY, USA. le.xie@northeastern.edu","institution_ids":["https://openalex.org/I121847817","https://openalex.org/I174216632"]},{"raw_affiliation_string":"School of Pharmacy and Pharmaceutical Sciences & Center for Drug Discovery, Northeastern University, Boston, 02115, MA, USA. le.xie@northeastern.edu","institution_ids":["https://openalex.org/I12912129"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5136526675","https://openalex.org/A5143765628","https://openalex.org/A5143817740"],"corresponding_institution_ids":["https://openalex.org/I121847817","https://openalex.org/I12912129","https://openalex.org/I174216632","https://openalex.org/I205783295","https://openalex.org/I39694355","https://openalex.org/I4210097825"],"apc_list":{"value":2190,"currency":"USD","value_usd":2190},"apc_paid":{"value":2190,"currency":"USD","value_usd":2190},"fwci":7.5613,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.97490855,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"18","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.36730000376701355,"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":0.36730000376701355,"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/T12534","display_name":"Protein Degradation and Inhibitors","score":0.1421000063419342,"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/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.08649999648332596,"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/kinetics","display_name":"Kinetics","score":0.5889999866485596},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.5827000141143799},{"id":"https://openalex.org/keywords/receptor\u2013ligand-kinetics","display_name":"Receptor\u2013ligand kinetics","score":0.5771999955177307},{"id":"https://openalex.org/keywords/plasma-protein-binding","display_name":"Plasma protein binding","score":0.3808000087738037},{"id":"https://openalex.org/keywords/binding-pocket","display_name":"Binding pocket","score":0.28839999437332153}],"concepts":[{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.652899980545044},{"id":"https://openalex.org/C148898269","wikidata":"https://www.wikidata.org/wiki/Q1108792","display_name":"Kinetics","level":2,"score":0.5889999866485596},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5827000141143799},{"id":"https://openalex.org/C152900378","wikidata":"https://www.wikidata.org/wiki/Q7302366","display_name":"Receptor\u2013ligand kinetics","level":3,"score":0.5771999955177307},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.39399999380111694},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.3808000087738037},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3262999951839447},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3262999951839447},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.29179999232292175},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.29109999537467957},{"id":"https://openalex.org/C3020299119","wikidata":"https://www.wikidata.org/wiki/Q423026","display_name":"Binding pocket","level":3,"score":0.28839999437332153},{"id":"https://openalex.org/C3018795828","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Binding affinities","level":3,"score":0.27379998564720154}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1186/s13321-026-01227-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-026-01227-0","pdf_url":null,"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:42163392","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42163392","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":"Journal Article"}],"best_oa_location":{"id":"doi:10.1186/s13321-026-01227-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-026-01227-0","pdf_url":null,"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/G2084843990","display_name":"AI-powered chemical proteomics for drug discovery targeting orphan proteins","funder_award_id":"2r01gm122845-05","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2839143310","display_name":"I-Corps: Novel molecule discovery by precisely predicting and modulating human pathology","funder_award_id":"2230354","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":84,"referenced_works":["https://openalex.org/W1975147762","https://openalex.org/W1975732928","https://openalex.org/W1980969309","https://openalex.org/W1983194490","https://openalex.org/W1986240377","https://openalex.org/W1988037271","https://openalex.org/W1993046136","https://openalex.org/W2006932016","https://openalex.org/W2016408686","https://openalex.org/W2018661561","https://openalex.org/W2028629022","https://openalex.org/W2060531713","https://openalex.org/W2151919617","https://openalex.org/W2164088236","https://openalex.org/W2169941775","https://openalex.org/W2265102996","https://openalex.org/W2266013672","https://openalex.org/W2295598076","https://openalex.org/W2346710580","https://openalex.org/W2594183968","https://openalex.org/W2617750324","https://openalex.org/W2770320302","https://openalex.org/W2781821160","https://openalex.org/W2785947426","https://openalex.org/W2804171113","https://openalex.org/W2887981960","https://openalex.org/W2900090807","https://openalex.org/W2902812092","https://openalex.org/W2963037989","https://openalex.org/W2974531988","https://openalex.org/W2986836624","https://openalex.org/W3007942792","https://openalex.org/W3009690250","https://openalex.org/W3012511738","https://openalex.org/W3018980093","https://openalex.org/W3019745511","https://openalex.org/W3028589594","https://openalex.org/W3032123378","https://openalex.org/W3042826782","https://openalex.org/W3090513030","https://openalex.org/W3096561213","https://openalex.org/W3105010031","https://openalex.org/W3116323439","https://openalex.org/W3140655290","https://openalex.org/W3165603781","https://openalex.org/W3167575787","https://openalex.org/W3168430821","https://openalex.org/W3177828909","https://openalex.org/W3197082762","https://openalex.org/W3215525389","https://openalex.org/W4200139236","https://openalex.org/W4200547951","https://openalex.org/W4210842338","https://openalex.org/W4214530112","https://openalex.org/W4281558021","https://openalex.org/W4283010692","https://openalex.org/W4290998851","https://openalex.org/W4297837492","https://openalex.org/W4313367649","https://openalex.org/W4317776906","https://openalex.org/W4318981550","https://openalex.org/W4322732093","https://openalex.org/W4327550249","https://openalex.org/W4361295032","https://openalex.org/W4367042263","https://openalex.org/W4379929801","https://openalex.org/W4387164156","https://openalex.org/W4387761568","https://openalex.org/W4388412569","https://openalex.org/W4389076414","https://openalex.org/W4389993920","https://openalex.org/W4391542588","https://openalex.org/W4391747328","https://openalex.org/W4399731549","https://openalex.org/W4399746375","https://openalex.org/W4399849668","https://openalex.org/W4402511830","https://openalex.org/W4403789768","https://openalex.org/W4406328702","https://openalex.org/W4407389375","https://openalex.org/W4411463597","https://openalex.org/W4417466821","https://openalex.org/W7128620109","https://openalex.org/W7133244980"],"related_works":[],"abstract_inverted_index":{"Accurately":[0],"characterizing":[1],"protein-ligand":[2,42,62,87,103,111,205,210,243],"binding,":[3],"such":[4,162],"as":[5,163,216,249,251],"binding":[6,63,88,121,144,164,167,206,211,277,285],"site,":[7],"affinity":[8,165,286],"and":[9,37,54,68,76,94,113,142,166,179,201,224,245,275,280,287],"kinetics,":[10],"is":[11,214],"critical":[12],"for":[13,188,204,227,261,295],"accelerating":[14],"drug":[15,192,296],"discovery.":[16,297],"However,":[17],"many":[18],"existing":[19],"computational":[20],"methods":[21,138],"face":[22],"key":[23],"limitations,":[24],"including":[25,120,236],"insufficient":[26],"integration":[27],"of":[28,33,40,61,118,175],"comprehensive":[29],"databases,":[30],"inadequate":[31],"representation":[32],"protein":[34,67,247],"structural":[35,128],"dynamics,":[36,248],"incomplete":[38],"modeling":[39],"microscale":[41,110,242],"interactions.":[43],"To":[44],"address":[45],"these":[46],"challenges,":[47],"we":[48],"introduce":[49],"ProMoNet,":[50,197],"a":[51,82,198,217,237,252,292],"sequence-based":[52,199],"pre-training":[53,83,106,200,218,238],"fine-tuning":[55,151,202,253],"framework":[56,203],"to":[57,72,97,159,220,266],"enhance":[58,77],"the":[59,115,156,258],"prediction":[60,100,213],"characteristics.":[64],"ProMoNet":[65,269],"leverages":[66],"molecular":[69],"foundation":[70],"models":[71,109,241],"expand":[73],"data":[74],"coverage":[75],"diversity.":[78],"It":[79],"also":[80],"introduces":[81],"strategy":[84,219],"based":[85],"on":[86,126],"site":[89,122,212,278],"prediction,":[90,169,208,289],"which":[91],"bridges":[92],"protein-":[93,223],"ligand-level":[95,225],"representations":[96,226,260],"support":[98],"downstream":[99,160,228,262],"tasks":[101,161,184],"involving":[102],"complexes.":[104],"Our":[105,150],"module":[107,132,152,239,254],"effectively":[108],"interactions":[112,244],"captures":[114,246],"dynamic":[116],"nature":[117],"proteins,":[119],"crypticity,":[123],"without":[124],"relying":[125],"3-dimensional":[127],"inputs.":[129],"Notably,":[130],"this":[131],"surpasses":[133],"or":[134],"matches":[135,270],"state-of-the-art":[136,271],"structure-based":[137,267],"in":[139,191,273,284],"identifying":[140],"exposed":[141,274],"cryptic":[143,276],"sites":[145],"while":[146],"maintaining":[147],"high":[148],"efficiency.":[149],"then":[153],"efficiently":[154,256],"transfers":[155],"pre-trained":[157,259],"knowledge":[158],"kinetics":[168,288],"achieving":[170],"superior":[171,282],"performance.":[172],"The":[173],"combination":[174],"ProMoNet's":[176],"strong":[177],"performance":[178,272],"demonstrated":[180],"efficiency":[181],"across":[182],"multiple":[183],"highlights":[185],"its":[186],"potential":[187],"broad":[189],"applications":[190],"discovery.Scientific":[193],"Contribution":[194],"We":[195,231],"propose":[196],"characteristic":[207],"where":[209],"introduced":[215],"bridge":[221],"independent":[222],"complex-level":[229],"tasks.":[230,263],"design":[232],"two":[233],"dedicated":[234],"modules,":[235],"that":[240,255],"well":[250],"integrates":[257],"Even":[264],"compared":[265],"methods,":[268],"identification":[279],"delivers":[281],"results":[283],"making":[290],"it":[291],"promising":[293],"tool":[294]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2026-05-21T00:00:00"}