{"id":"https://openalex.org/W4383894404","doi":"https://doi.org/10.1088/2632-2153/ace67b","title":"Prediction of molecular field points using SE(3)-transformer model","display_name":"Prediction of molecular field points using SE(3)-transformer model","publication_year":2023,"publication_date":"2023-07-11","ids":{"openalex":"https://openalex.org/W4383894404","doi":"https://doi.org/10.1088/2632-2153/ace67b"},"language":"en","primary_location":{"id":"doi:10.1088/2632-2153/ace67b","is_oa":true,"landing_page_url":"https://doi.org/10.1088/2632-2153/ace67b","pdf_url":"https://iopscience.iop.org/article/10.1088/2632-2153/ace67b/pdf","source":{"id":"https://openalex.org/S4210200687","display_name":"Machine Learning Science and Technology","issn_l":"2632-2153","issn":["2632-2153"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320083","host_organization_name":"IOP Publishing","host_organization_lineage":["https://openalex.org/P4310320083","https://openalex.org/P4310311669"],"host_organization_lineage_names":["IOP Publishing","Institute of Physics"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Machine Learning: Science and Technology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://iopscience.iop.org/article/10.1088/2632-2153/ace67b/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5098532881","display_name":"Florian B Hinz","orcid":null},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Florian B Hinz","raw_affiliation_strings":["Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel, Basel-Stadt, 4056, SWITZERLAND"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel, Basel-Stadt, 4056, SWITZERLAND","institution_ids":["https://openalex.org/I1850255"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101138262","display_name":"Amr H. Mahmoud","orcid":null},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Amr H Mahmoud","raw_affiliation_strings":["Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel, Basel-Stadt, 4056, SWITZERLAND"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel, Basel-Stadt, 4056, SWITZERLAND","institution_ids":["https://openalex.org/I1850255"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041891399","display_name":"Markus A. Lill","orcid":"https://orcid.org/0000-0003-3023-5188"},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Markus A Lill","raw_affiliation_strings":["Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel, 4056, SWITZERLAND"],"raw_orcid":"https://orcid.org/0000-0003-3023-5188","affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel, 4056, SWITZERLAND","institution_ids":["https://openalex.org/I1850255"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5041891399"],"corresponding_institution_ids":["https://openalex.org/I1850255"],"apc_list":{"value":1600,"currency":"GBP","value_usd":1962},"apc_paid":{"value":1600,"currency":"GBP","value_usd":1962},"fwci":0.3794,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.63750292,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"4","issue":"3","first_page":"035016","last_page":"035016"},"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9998000264167786,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9961000084877014,"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/maxima-and-minima","display_name":"Maxima and minima","score":0.6977766752243042},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5720946192741394},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.46578067541122437},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4268674850463867},{"id":"https://openalex.org/keywords/grid","display_name":"Grid","score":0.42351579666137695},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.42051243782043457},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.34963294863700867},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17124342918395996}],"concepts":[{"id":"https://openalex.org/C186633575","wikidata":"https://www.wikidata.org/wiki/Q845060","display_name":"Maxima and minima","level":2,"score":0.6977766752243042},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5720946192741394},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.46578067541122437},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4268674850463867},{"id":"https://openalex.org/C187691185","wikidata":"https://www.wikidata.org/wiki/Q2020720","display_name":"Grid","level":2,"score":0.42351579666137695},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.42051243782043457},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.34963294863700867},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17124342918395996},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1088/2632-2153/ace67b","is_oa":true,"landing_page_url":"https://doi.org/10.1088/2632-2153/ace67b","pdf_url":"https://iopscience.iop.org/article/10.1088/2632-2153/ace67b/pdf","source":{"id":"https://openalex.org/S4210200687","display_name":"Machine Learning Science and Technology","issn_l":"2632-2153","issn":["2632-2153"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320083","host_organization_name":"IOP Publishing","host_organization_lineage":["https://openalex.org/P4310320083","https://openalex.org/P4310311669"],"host_organization_lineage_names":["IOP Publishing","Institute of Physics"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Machine Learning: Science and Technology","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:3bd870e33d974b64bfa2a6093590b630","is_oa":true,"landing_page_url":"https://doaj.org/article/3bd870e33d974b64bfa2a6093590b630","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":"Machine Learning: Science and Technology, Vol 4, Iss 3, p 035016 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1088/2632-2153/ace67b","is_oa":true,"landing_page_url":"https://doi.org/10.1088/2632-2153/ace67b","pdf_url":"https://iopscience.iop.org/article/10.1088/2632-2153/ace67b/pdf","source":{"id":"https://openalex.org/S4210200687","display_name":"Machine Learning Science and Technology","issn_l":"2632-2153","issn":["2632-2153"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320083","host_organization_name":"IOP Publishing","host_organization_lineage":["https://openalex.org/P4310320083","https://openalex.org/P4310311669"],"host_organization_lineage_names":["IOP Publishing","Institute of Physics"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Machine Learning: Science and Technology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.75,"display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G2639422791","display_name":null,"funder_award_id":"310030_197629","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4383894404.pdf"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1972155638","https://openalex.org/W2044834685","https://openalex.org/W2081322171","https://openalex.org/W2086477891","https://openalex.org/W2097307439","https://openalex.org/W2101234009","https://openalex.org/W2112796928","https://openalex.org/W2788775653","https://openalex.org/W3036737467","https://openalex.org/W4297688279","https://openalex.org/W4379446006","https://openalex.org/W6694954494","https://openalex.org/W6749031613","https://openalex.org/W6779789776","https://openalex.org/W6795525955"],"related_works":["https://openalex.org/W2375684291","https://openalex.org/W2354676191","https://openalex.org/W3188646203","https://openalex.org/W136674370","https://openalex.org/W2909957174","https://openalex.org/W2105527480","https://openalex.org/W4320035781","https://openalex.org/W2052387497","https://openalex.org/W4246278799","https://openalex.org/W2050203848"],"abstract_inverted_index":{"Abstract":[0],"Due":[1],"to":[2,41,72,181],"their":[3],"computational":[4],"efficiency,":[5,60],"2D":[6,37],"fingerprints":[7],"are":[8,70,109,150],"typically":[9],"used":[10,71],"in":[11,30,77],"similarity-based":[12],"high-content":[13,125],"screening.":[14,126],"The":[15,79],"interaction":[16,50,57,89],"of":[17,63,81,87,115,121,135,167,178,193,201],"a":[18,95,100,164,198],"ligand":[19,75,93],"with":[20,35,169],"its":[21,27],"target":[22],"protein,":[23],"however,":[24],"relies":[25],"on":[26,99,143,163],"physicochemical":[28],"interactions":[29],"3D":[31],"space.":[32],"Thus,":[33],"ligands":[34,47,168],"different":[36],"scaffolds":[38],"can":[39,54],"bind":[40],"the":[42,61,74,85,88,92,104,144,176,194],"same":[43],"protein":[44],"if":[45],"these":[46],"share":[48],"similar":[49],"patterns.":[51],"Molecular":[52],"fields":[53],"represent":[55],"those":[56,64],"profiles.":[58],"For":[59],"extrema":[62],"molecular":[65,105,145],"fields,":[66],"named":[67],"field":[68,82,118,136,170,188],"points,":[69],"quantify":[73],"similarity":[76],"3D.":[78],"calculation":[80],"points":[83,137,149,189],"involves":[84],"evaluation":[86],"energy":[90],"between":[91],"and":[94,186],"small":[96],"probe":[97],"shifted":[98],"fine":[101],"grid":[102],"representing":[103],"surface.":[106],"These":[107],"calculations":[108],"computationally":[110],"prohibitive":[111],"for":[112,124,197],"large":[113,165],"datasets":[114],"ligands,":[116],"making":[117],"point":[119,171],"representations":[120],"molecules":[122],"intractable":[123],"Here,":[127],"we":[128],"overcome":[129],"this":[130,179],"roadblock":[131],"by":[132,152],"one-shot":[133],"prediction":[134],"using":[138],"generative":[139],"neural":[140,160],"networks":[141],"based":[142],"structure":[146],"alone.":[147],"Field":[148],"predicted":[151],"training":[153],"an":[154,156],"SE(3)-Transformer,":[155],"equivariant,":[157],"attention-based":[158],"graph":[159],"network":[161],"architecture,":[162],"set":[166,200],"data.":[172],"Resulting":[173],"data":[174],"demonstrates":[175],"feasibility":[177],"approach":[180],"precisely":[182],"generate":[183],"negative,":[184],"positive":[185],"hydrophobic":[187],"within":[190],"0.5":[191],"\u00c5":[192],"ground":[195],"truth":[196],"diverse":[199],"drug-like":[202],"molecules.":[203]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
