{"id":"https://openalex.org/W4388627827","doi":"https://doi.org/10.1038/s42256-023-00756-9","title":"Learning characteristics of graph neural networks predicting protein\u2013ligand affinities","display_name":"Learning characteristics of graph neural networks predicting protein\u2013ligand affinities","publication_year":2023,"publication_date":"2023-11-13","ids":{"openalex":"https://openalex.org/W4388627827","doi":"https://doi.org/10.1038/s42256-023-00756-9"},"language":"en","primary_location":{"id":"doi:10.1038/s42256-023-00756-9","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s42256-023-00756-9","pdf_url":null,"source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Machine Intelligence","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002268567","display_name":"Andrea Mastropietro","orcid":"https://orcid.org/0000-0002-3456-9428"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]},{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["DE","IT"],"is_corresponding":false,"raw_author_name":"Andrea Mastropietro","raw_affiliation_strings":["Department of Computer, Control and Management Engineering \u2018Antonio Ruberti\u2019 (DIAG), Sapienza University of Rome, Rome, Italy","Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universit\u00e4t, Bonn, Germany"],"raw_orcid":"https://orcid.org/0000-0002-3456-9428","affiliations":[{"raw_affiliation_string":"Department of Computer, Control and Management Engineering \u2018Antonio Ruberti\u2019 (DIAG), Sapienza University of Rome, Rome, Italy","institution_ids":["https://openalex.org/I861853513"]},{"raw_affiliation_string":"Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universit\u00e4t, Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078075375","display_name":"Giuseppe Pasculli","orcid":"https://orcid.org/0000-0002-0499-2292"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giuseppe Pasculli","raw_affiliation_strings":["Department of Computer, Control and Management Engineering \u2018Antonio Ruberti\u2019 (DIAG), Sapienza University of Rome, Rome, Italy"],"raw_orcid":"https://orcid.org/0000-0002-0499-2292","affiliations":[{"raw_affiliation_string":"Department of Computer, Control and Management Engineering \u2018Antonio Ruberti\u2019 (DIAG), Sapienza University of Rome, Rome, Italy","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039926688","display_name":"J\u00fcrgen Bajorath","orcid":"https://orcid.org/0000-0002-0557-5714"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]},{"id":"https://openalex.org/I4387154616","display_name":"Lamarr Institute for Machine Learning and Artificial Intelligence","ror":"https://ror.org/04s11ea33","country_code":null,"type":"facility","lineage":["https://openalex.org/I135140700","https://openalex.org/I200332995","https://openalex.org/I4210098062","https://openalex.org/I4210144576","https://openalex.org/I4387154616","https://openalex.org/I4923324","https://openalex.org/I4923324"]},{"id":"https://openalex.org/I4923324","display_name":"Fraunhofer-Gesellschaft","ror":"https://ror.org/05hkkdn48","country_code":"DE","type":"government","lineage":["https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"J\u00fcrgen Bajorath","raw_affiliation_strings":["Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universit\u00e4t, Bonn, Germany","Lamarr Institute for Machine Learning and Artificial Intelligence, Bonn, Germany"],"raw_orcid":"https://orcid.org/0000-0002-0557-5714","affiliations":[{"raw_affiliation_string":"Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universit\u00e4t, Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]},{"raw_affiliation_string":"Lamarr Institute for Machine Learning and Artificial Intelligence, Bonn, Germany","institution_ids":["https://openalex.org/I4387154616","https://openalex.org/I4923324"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5039926688"],"corresponding_institution_ids":["https://openalex.org/I135140700","https://openalex.org/I4387154616","https://openalex.org/I4923324"],"apc_list":{"value":11690,"currency":"USD","value_usd":11690},"apc_paid":null,"fwci":9.9047,"has_fulltext":false,"cited_by_count":71,"citation_normalized_percentile":{"value":0.98733123,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"5","issue":"12","first_page":"1427","last_page":"1436"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9939000010490417,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9883000254631042,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/affinities","display_name":"Affinities","score":0.697670042514801},{"id":"https://openalex.org/keywords/memorization","display_name":"Memorization","score":0.6846920251846313},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6100875735282898},{"id":"https://openalex.org/keywords/protein-ligand","display_name":"Protein ligand","score":0.6018831133842468},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.5770964622497559},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5512842535972595},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4893738627433777},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4298904538154602},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.41787591576576233},{"id":"https://openalex.org/keywords/relevance","display_name":"Relevance (law)","score":0.4150456190109253},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.389192134141922},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.26490288972854614},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.26035362482070923},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21638014912605286},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.18778619170188904},{"id":"https://openalex.org/keywords/cognitive-psychology","display_name":"Cognitive psychology","score":0.12269338965415955},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.12099528312683105},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.09250923991203308}],"concepts":[{"id":"https://openalex.org/C2780283098","wikidata":"https://www.wikidata.org/wiki/Q4688960","display_name":"Affinities","level":2,"score":0.697670042514801},{"id":"https://openalex.org/C30038468","wikidata":"https://www.wikidata.org/wiki/Q4354775","display_name":"Memorization","level":2,"score":0.6846920251846313},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6100875735282898},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.6018831133842468},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5770964622497559},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5512842535972595},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4893738627433777},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4298904538154602},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.41787591576576233},{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.4150456190109253},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.389192134141922},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.26490288972854614},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.26035362482070923},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21638014912605286},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.18778619170188904},{"id":"https://openalex.org/C180747234","wikidata":"https://www.wikidata.org/wiki/Q23373","display_name":"Cognitive psychology","level":1,"score":0.12269338965415955},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.12099528312683105},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.09250923991203308},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1038/s42256-023-00756-9","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s42256-023-00756-9","pdf_url":null,"source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Machine Intelligence","raw_type":"journal-article"},{"id":"pmh:oai:iris.uniroma1.it:11573/1691854","is_oa":false,"landing_page_url":"https://hdl.handle.net/11573/1691854","pdf_url":null,"source":{"id":"https://openalex.org/S4377196107","display_name":"IRIS Research product catalog (Sapienza University of Rome)","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W1908851533","https://openalex.org/W1964357740","https://openalex.org/W1977458743","https://openalex.org/W1988195734","https://openalex.org/W1993046136","https://openalex.org/W2012887432","https://openalex.org/W2041877730","https://openalex.org/W2073021822","https://openalex.org/W2114162221","https://openalex.org/W2116341502","https://openalex.org/W2132022337","https://openalex.org/W2146940292","https://openalex.org/W2487898712","https://openalex.org/W2587598315","https://openalex.org/W2738737407","https://openalex.org/W2763936395","https://openalex.org/W2781821160","https://openalex.org/W2784213390","https://openalex.org/W2893435209","https://openalex.org/W2919115771","https://openalex.org/W2921802966","https://openalex.org/W2937307539","https://openalex.org/W2962711740","https://openalex.org/W2962810718","https://openalex.org/W2964015378","https://openalex.org/W2964121744","https://openalex.org/W2964677890","https://openalex.org/W2970971581","https://openalex.org/W3001433048","https://openalex.org/W3005552578","https://openalex.org/W3020257619","https://openalex.org/W3096561213","https://openalex.org/W3116202926","https://openalex.org/W3130218089","https://openalex.org/W3140330522","https://openalex.org/W3156998432","https://openalex.org/W3185256938","https://openalex.org/W3201055938","https://openalex.org/W4210307613","https://openalex.org/W4210310710","https://openalex.org/W4281381643","https://openalex.org/W4288419263","https://openalex.org/W4293581802","https://openalex.org/W4295547865","https://openalex.org/W4297733535","https://openalex.org/W4310011599","https://openalex.org/W6675354045","https://openalex.org/W6894159969","https://openalex.org/W6912665681"],"related_works":["https://openalex.org/W3093895509","https://openalex.org/W4241081643","https://openalex.org/W1974414168","https://openalex.org/W3163481960","https://openalex.org/W2323394100","https://openalex.org/W280704926","https://openalex.org/W2476068070","https://openalex.org/W1485106526","https://openalex.org/W3008230527","https://openalex.org/W3131522312"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":15},{"year":2025,"cited_by_count":33},{"year":2024,"cited_by_count":22},{"year":2023,"cited_by_count":1}],"updated_date":"2026-08-12T21:12:35.861297","created_date":"2025-10-10T00:00:00"}
