{"id":"https://openalex.org/W4224058524","doi":"https://doi.org/10.1021/acs.jcim.2c00260","title":"Accurate Prediction of Aqueous Free Solvation Energies Using 3D Atomic Feature-Based Graph Neural Network with Transfer Learning","display_name":"Accurate Prediction of Aqueous Free Solvation Energies Using 3D Atomic Feature-Based Graph Neural Network with Transfer Learning","publication_year":2022,"publication_date":"2022-04-14","ids":{"openalex":"https://openalex.org/W4224058524","doi":"https://doi.org/10.1021/acs.jcim.2c00260","pmid":"https://pubmed.ncbi.nlm.nih.gov/35422122"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c00260","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00260","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9038704","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100416369","display_name":"Dongdong Zhang","orcid":"https://orcid.org/0000-0001-9489-7995"},"institutions":[{"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":false,"raw_author_name":"Dongdong Zhang","raw_affiliation_strings":["Department of Chemistry, New York University, New York, New York 10003, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, New York University, New York, New York 10003, United States","institution_ids":["https://openalex.org/I57206974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087490418","display_name":"Song Xia","orcid":"https://orcid.org/0000-0002-1962-4273"},"institutions":[{"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":false,"raw_author_name":"Song Xia","raw_affiliation_strings":["Department of Chemistry, New York University, New York, New York 10003, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, New York University, New York, New York 10003, United States","institution_ids":["https://openalex.org/I57206974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063629758","display_name":"Yingkai Zhang","orcid":"https://orcid.org/0000-0002-4984-3354"},"institutions":[{"id":"https://openalex.org/I258800397","display_name":"New York University Shanghai","ror":"https://ror.org/02vpsdb40","country_code":"CN","type":"education","lineage":["https://openalex.org/I258800397","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":["CN","US"],"is_corresponding":true,"raw_author_name":"Yingkai Zhang","raw_affiliation_strings":["Department of Chemistry, New York University, New York, New York 10003, United States","NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China"],"raw_orcid":"https://orcid.org/0000-0002-4984-3354","affiliations":[{"raw_affiliation_string":"Department of Chemistry, New York University, New York, New York 10003, United States","institution_ids":["https://openalex.org/I57206974"]},{"raw_affiliation_string":"NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China","institution_ids":["https://openalex.org/I258800397"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5063629758"],"corresponding_institution_ids":["https://openalex.org/I258800397","https://openalex.org/I57206974"],"apc_list":null,"apc_paid":null,"fwci":3.7634,"has_fulltext":false,"cited_by_count":57,"citation_normalized_percentile":{"value":0.94987225,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"62","issue":"8","first_page":"1840","last_page":"1848"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":1.0,"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"}},"topics":[{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":1.0,"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"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9997000098228455,"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":0.9872999787330627,"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/solvation","display_name":"Solvation","score":0.8706651926040649},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6152670979499817},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.6100828051567078},{"id":"https://openalex.org/keywords/molecular-graph","display_name":"Molecular graph","score":0.5573968887329102},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4900394678115845},{"id":"https://openalex.org/keywords/mean-squared-error","display_name":"Mean squared error","score":0.452690452337265},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4401856064796448},{"id":"https://openalex.org/keywords/data-set","display_name":"Data set","score":0.4182394742965698},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.37518900632858276},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3563781976699829},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.33827972412109375},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.20622634887695312},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.20050492882728577},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17097654938697815}],"concepts":[{"id":"https://openalex.org/C148093993","wikidata":"https://www.wikidata.org/wiki/Q739398","display_name":"Solvation","level":3,"score":0.8706651926040649},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6152670979499817},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.6100828051567078},{"id":"https://openalex.org/C2780022179","wikidata":"https://www.wikidata.org/wiki/Q1986794","display_name":"Molecular graph","level":3,"score":0.5573968887329102},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4900394678115845},{"id":"https://openalex.org/C139945424","wikidata":"https://www.wikidata.org/wiki/Q1940696","display_name":"Mean squared error","level":2,"score":0.452690452337265},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4401856064796448},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.4182394742965698},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.37518900632858276},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3563781976699829},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.33827972412109375},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.20622634887695312},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.20050492882728577},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17097654938697815},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","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":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.2c00260","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00260","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:35422122","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35422122","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 chemical information and modeling","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9038704","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9038704","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:9038704","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9038704","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.7400000095367432,"display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G6179976271","display_name":null,"funder_award_id":"R35 GM127040","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6976097973","display_name":null,"funder_award_id":"R35-GM127040","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":55,"referenced_works":["https://openalex.org/W572193077","https://openalex.org/W1975997599","https://openalex.org/W1993395512","https://openalex.org/W2008505552","https://openalex.org/W2011215428","https://openalex.org/W2068465600","https://openalex.org/W2121853844","https://openalex.org/W2143981217","https://openalex.org/W2162235098","https://openalex.org/W2169527365","https://openalex.org/W2188555324","https://openalex.org/W2244785476","https://openalex.org/W2290847742","https://openalex.org/W2322826137","https://openalex.org/W2324718891","https://openalex.org/W2527189750","https://openalex.org/W2562301581","https://openalex.org/W2589948472","https://openalex.org/W2592364803","https://openalex.org/W2593436234","https://openalex.org/W2594183968","https://openalex.org/W2606780347","https://openalex.org/W2735246657","https://openalex.org/W2764264130","https://openalex.org/W2891365537","https://openalex.org/W2901003004","https://openalex.org/W2950128007","https://openalex.org/W2961051133","https://openalex.org/W2962711740","https://openalex.org/W2964917722","https://openalex.org/W2966357564","https://openalex.org/W2968734407","https://openalex.org/W2969679365","https://openalex.org/W2976720228","https://openalex.org/W2998374989","https://openalex.org/W3005552578","https://openalex.org/W3007488165","https://openalex.org/W3016124664","https://openalex.org/W3016983547","https://openalex.org/W3032781902","https://openalex.org/W3035813050","https://openalex.org/W3042826782","https://openalex.org/W3100157108","https://openalex.org/W3116202926","https://openalex.org/W3117876228","https://openalex.org/W3118102630","https://openalex.org/W3129238601","https://openalex.org/W3132572925","https://openalex.org/W3134146005","https://openalex.org/W3134184520","https://openalex.org/W3151248499","https://openalex.org/W3166272013","https://openalex.org/W3186935805","https://openalex.org/W4241002118","https://openalex.org/W4288419263"],"related_works":["https://openalex.org/W2067207114","https://openalex.org/W2143156304","https://openalex.org/W1521945250","https://openalex.org/W1992757523","https://openalex.org/W4254536785","https://openalex.org/W1996895506","https://openalex.org/W3012401792","https://openalex.org/W2503236658","https://openalex.org/W1570292012","https://openalex.org/W2808877228"],"abstract_inverted_index":{"Graph":[0],"neural":[1],"network":[2],"(GNN)-based":[3],"deep":[4],"learning":[5,104,120],"(DL)":[6],"models":[7,108,188],"have":[8],"been":[9],"widely":[10],"implemented":[11],"to":[12,30,39,184],"predict":[13],"the":[14,31,84,103,133,139,144,148],"experimental":[15,35,135],"aqueous":[16,55],"solvation":[17,56,112],"free":[18,57,113],"energy,":[19],"while":[20],"its":[21],"prediction":[22,146,187],"accuracy":[23,64],"has":[24],"reached":[25],"a":[26,46,76,118,153,160,181],"plateau":[27],"partly":[28],"due":[29],"scarcity":[32],"of":[33,54,106,156,163],"available":[34],"data.":[36],"In":[37],"order":[38],"tackle":[40],"this":[41],"challenge,":[42],"we":[43,74,116],"first":[44],"build":[45],"large":[47],"and":[48,63,89,129,138,159,177,195],"diverse":[49],"calculated":[50,111],"data":[51,136,150,168,196],"set":[52,151],"Frag20-Aqsol-100K":[53,128],"energy":[58],"with":[59,69,83,152],"reasonable":[60],"computational":[61],"cost":[62],"via":[65],"electronic":[66],"structure":[67],"calculations":[68],"continuum":[70],"solvent":[71],"models.":[72],"Then,":[73],"develop":[75,185],"novel":[77],"3D":[78,92],"atomic":[79,93],"feature-based":[80],"GNN":[81,107],"model":[82,126,141],"principal":[85],"neighborhood":[86],"aggregation":[87],"(PNAConv)":[88],"demonstrate":[90],"that":[91,173],"features":[94],"obtained":[95],"from":[96],"molecular":[97,175,190],"mechanics-optimized":[98],"geometries":[99],"can":[100],"significantly":[101],"improve":[102],"power":[105],"in":[109,189],"predicting":[110],"energies.":[114],"Finally,":[115],"employ":[117],"transfer":[119],"strategy":[121,183],"by":[122],"pre-training":[123],"our":[124],"DL":[125,178],"on":[127,132,147],"fine-tuning":[130],"it":[131],"small":[134],"set,":[137],"fine-tuned":[140],"A3D-PNAConv-FT":[142],"achieves":[143],"state-of-the-art":[145],"FreeSolv":[149],"root-mean-squared":[154],"error":[155,162],"0.719":[157],"kcal/mol":[158,165],"mean-absolute":[161],"0.417":[164],"using":[166],"random":[167],"splits.":[169],"These":[170],"results":[171],"indicate":[172],"integrating":[174],"modeling":[176],"would":[179],"be":[180],"promising":[182],"robust":[186],"science.":[191],"The":[192],"source":[193],"code":[194],"are":[197],"accessible":[198],"at:":[199],"https://yzhang.hpc.nyu.edu/IMA.":[200]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":15},{"year":2023,"cited_by_count":20},{"year":2022,"cited_by_count":10}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}