{"id":"https://openalex.org/W3087318293","doi":"https://doi.org/10.1186/s13321-020-00460-5","title":"Molecular representations in AI-driven drug discovery: a review and practical guide","display_name":"Molecular representations in AI-driven drug discovery: a review and practical guide","publication_year":2020,"publication_date":"2020-09-17","ids":{"openalex":"https://openalex.org/W3087318293","doi":"https://doi.org/10.1186/s13321-020-00460-5","mag":"3087318293","pmid":"https://pubmed.ncbi.nlm.nih.gov/33431035"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-020-00460-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-020-00460-5","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-020-00460-5","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-020-00460-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006768343","display_name":"Laurianne David","orcid":"https://orcid.org/0000-0002-6455-1958"},"institutions":[{"id":"https://openalex.org/I4210128490","display_name":"AstraZeneca (Japan)","ror":"https://ror.org/047k23798","country_code":"JP","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210128490"]},{"id":"https://openalex.org/I4210137263","display_name":"AstraZeneca (Finland)","ror":"https://ror.org/035n56j11","country_code":"FI","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210137263"]},{"id":"https://openalex.org/I4210159719","display_name":"AstraZeneca (Germany)","ror":"https://ror.org/054q96n74","country_code":"DE","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210159719"]}],"countries":["DE","FI","JP"],"is_corresponding":true,"raw_author_name":"Laurianne David","raw_affiliation_strings":["Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, Astrazeneca Gothenburg, Sweden. laurianne.david1@gmail.com","Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, Astrazeneca Gothenburg, Sweden"],"raw_orcid":"https://orcid.org/0000-0002-6455-1958","affiliations":[{"raw_affiliation_string":"Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, Astrazeneca Gothenburg, Sweden. laurianne.david1@gmail.com","institution_ids":["https://openalex.org/I4210128490","https://openalex.org/I4210137263","https://openalex.org/I4210159719"]},{"raw_affiliation_string":"Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, Astrazeneca Gothenburg, Sweden","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021552278","display_name":"Amol Thakkar","orcid":"https://orcid.org/0000-0003-0403-4067"},"institutions":[{"id":"https://openalex.org/I118564535","display_name":"University of Bern","ror":"https://ror.org/02k7v4d05","country_code":"CH","type":"education","lineage":["https://openalex.org/I118564535"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Amol Thakkar","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland","Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, Astrazeneca Gothenburg, Sweden"],"raw_orcid":"https://orcid.org/0000-0003-0403-4067","affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland","institution_ids":["https://openalex.org/I118564535"]},{"raw_affiliation_string":"Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, Astrazeneca Gothenburg, Sweden","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090993508","display_name":"Roc\u00edo Mercado","orcid":"https://orcid.org/0000-0002-6170-6088"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Roc\u00edo Mercado","raw_affiliation_strings":["Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, Astrazeneca Gothenburg, Sweden"],"raw_orcid":"https://orcid.org/0000-0002-6170-6088","affiliations":[{"raw_affiliation_string":"Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, Astrazeneca Gothenburg, Sweden","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076975589","display_name":"Ola Engkvist","orcid":"https://orcid.org/0000-0003-4970-6461"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ola Engkvist","raw_affiliation_strings":["Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, Astrazeneca Gothenburg, Sweden"],"raw_orcid":"https://orcid.org/0000-0003-4970-6461","affiliations":[{"raw_affiliation_string":"Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, Astrazeneca Gothenburg, Sweden","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5006768343"],"corresponding_institution_ids":["https://openalex.org/I4210128490","https://openalex.org/I4210137263","https://openalex.org/I4210159719"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":40.495,"has_fulltext":true,"cited_by_count":559,"citation_normalized_percentile":{"value":0.99863178,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"12","issue":"1","first_page":"56","last_page":"56"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9961000084877014,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9873999953269958,"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/drug-discovery","display_name":"Drug discovery","score":0.7380412220954895},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.661443829536438},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5857212543487549},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.21431654691696167},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.06762313842773438}],"concepts":[{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.7380412220954895},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.661443829536438},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5857212543487549},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.21431654691696167},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.06762313842773438}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-020-00460-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-020-00460-5","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-020-00460-5","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:33431035","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33431035","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":null},{"id":"pmh:oai:doaj.org/article:95170f073bcc47b7be927a55fa9a529d","is_oa":true,"landing_page_url":"https://doaj.org/article/95170f073bcc47b7be927a55fa9a529d","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":"Journal of Cheminformatics, Vol 12, Iss 1, Pp 1-22 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7495975","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7495975","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-020-00460-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-020-00460-5","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-020-00460-5","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","license_id":"https://openalex.org/licenses/cc-by","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/G1002412395","display_name":"Big Data in Chemistry","funder_award_id":"676434","funder_id":"https://openalex.org/F4320338337","funder_display_name":"H2020 Marie Sk\u0142odowska-Curie Actions"}],"funders":[{"id":"https://openalex.org/F4320307770","display_name":"AstraZeneca","ror":"https://ror.org/04r9x1a08"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320338337","display_name":"H2020 Marie Sk\u0142odowska-Curie Actions","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3087318293.pdf","grobid_xml":"https://content.openalex.org/works/W3087318293.grobid-xml"},"referenced_works_count":142,"referenced_works":["https://openalex.org/W10340167","https://openalex.org/W178306723","https://openalex.org/W192706502","https://openalex.org/W575847245","https://openalex.org/W1508604947","https://openalex.org/W1525770891","https://openalex.org/W1531524766","https://openalex.org/W1607767610","https://openalex.org/W1971521451","https://openalex.org/W1975147762","https://openalex.org/W1975169446","https://openalex.org/W1980090013","https://openalex.org/W1982597534","https://openalex.org/W1982870104","https://openalex.org/W1983217234","https://openalex.org/W1983478747","https://openalex.org/W1983817726","https://openalex.org/W1988037271","https://openalex.org/W1994137238","https://openalex.org/W1996673984","https://openalex.org/W1998519205","https://openalex.org/W1998997530","https://openalex.org/W1999241626","https://openalex.org/W2002727413","https://openalex.org/W2014865312","https://openalex.org/W2020996919","https://openalex.org/W2027254946","https://openalex.org/W2028046413","https://openalex.org/W2028056984","https://openalex.org/W2029667189","https://openalex.org/W2031372687","https://openalex.org/W2032071738","https://openalex.org/W2033788780","https://openalex.org/W2037109408","https://openalex.org/W2040103915","https://openalex.org/W2043212464","https://openalex.org/W2043509228","https://openalex.org/W2044834685","https://openalex.org/W2046376233","https://openalex.org/W2048620093","https://openalex.org/W2051700505","https://openalex.org/W2051810242","https://openalex.org/W2052844914","https://openalex.org/W2059713851","https://openalex.org/W2060586571","https://openalex.org/W2061890234","https://openalex.org/W2072148103","https://openalex.org/W2083224653","https://openalex.org/W2086757166","https://openalex.org/W2091159078","https://openalex.org/W2094937489","https://openalex.org/W2096417508","https://openalex.org/W2103626206","https://openalex.org/W2105916282","https://openalex.org/W2109598625","https://openalex.org/W2110455859","https://openalex.org/W2112844927","https://openalex.org/W2116105292","https://openalex.org/W2128119041","https://openalex.org/W2130479394","https://openalex.org/W2134648236","https://openalex.org/W2135505477","https://openalex.org/W2139642094","https://openalex.org/W2145707967","https://openalex.org/W2149244170","https://openalex.org/W2155741020","https://openalex.org/W2170973067","https://openalex.org/W2173027866","https://openalex.org/W2200017991","https://openalex.org/W2225705146","https://openalex.org/W2316520129","https://openalex.org/W2326892341","https://openalex.org/W2405035126","https://openalex.org/W2482550502","https://openalex.org/W2533037805","https://openalex.org/W2561520829","https://openalex.org/W2567534979","https://openalex.org/W2580289839","https://openalex.org/W2586724023","https://openalex.org/W2591586569","https://openalex.org/W2604296437","https://openalex.org/W2607266785","https://openalex.org/W2611907395","https://openalex.org/W2622236128","https://openalex.org/W2627538532","https://openalex.org/W2734970798","https://openalex.org/W2735246657","https://openalex.org/W2743571801","https://openalex.org/W2747592475","https://openalex.org/W2770538422","https://openalex.org/W2773553108","https://openalex.org/W2786103815","https://openalex.org/W2786722833","https://openalex.org/W2790040331","https://openalex.org/W2790808809","https://openalex.org/W2803462582","https://openalex.org/W2805516822","https://openalex.org/W2883583109","https://openalex.org/W2886791556","https://openalex.org/W2901223208","https://openalex.org/W2902415322","https://openalex.org/W2903262661","https://openalex.org/W2903738757","https://openalex.org/W2904643020","https://openalex.org/W2905373823","https://openalex.org/W2907657781","https://openalex.org/W2943959866","https://openalex.org/W2947643486","https://openalex.org/W2950128007","https://openalex.org/W2950955377","https://openalex.org/W2952254971","https://openalex.org/W2962711740","https://openalex.org/W2963028280","https://openalex.org/W2963734039","https://openalex.org/W2966009035","https://openalex.org/W2966357564","https://openalex.org/W2973074478","https://openalex.org/W2974310638","https://openalex.org/W2975022113","https://openalex.org/W2982209755","https://openalex.org/W2987143844","https://openalex.org/W2988541550","https://openalex.org/W2989615256","https://openalex.org/W2989775272","https://openalex.org/W2991188715","https://openalex.org/W2992311071","https://openalex.org/W2994708127","https://openalex.org/W2999044305","https://openalex.org/W2999211744","https://openalex.org/W3000478925","https://openalex.org/W3009440197","https://openalex.org/W3011200991","https://openalex.org/W3102909511","https://openalex.org/W3202117332","https://openalex.org/W3202562506","https://openalex.org/W4206092243","https://openalex.org/W4231645939","https://openalex.org/W4238939225","https://openalex.org/W4245748464","https://openalex.org/W4249482084","https://openalex.org/W4288027837","https://openalex.org/W4300303686"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"The":[0],"technological":[1],"advances":[2],"of":[3,15,31,56,62,79,84,99,113,124,148,168,180],"the":[4,9,13,23,26,69,76,82,100,146,166,178],"past":[5],"century,":[6],"marked":[7],"by":[8,50,54],"computer":[10],"revolution":[11],"and":[12,29,52,81,92,105,171],"advent":[14],"high-throughput":[16],"screening":[17],"technologies":[18],"in":[19,43,109,127,150],"drug":[20,110,129,151],"discovery,":[21,111],"opened":[22],"path":[24],"to":[25,40,75,134,145,173],"computational":[27],"analysis":[28],"visualization":[30],"bioactive":[32],"molecules.":[33],"For":[34],"this":[35],"purpose,":[36],"it":[37],"became":[38],"necessary":[39],"represent":[41],"molecules":[42],"a":[44,86,136,157],"syntax":[45],"that":[46,88,142],"would":[47],"be":[48],"readable":[49],"computers":[51,80],"understandable":[53],"scientists":[55],"various":[57],"fields.":[58,182],"A":[59],"large":[60],"number":[61],"chemical":[63,93,169],"representations":[64,107,126,141,170],"have":[65,162],"been":[66],"developed":[67],"over":[68],"years,":[70],"their":[71],"numerosity":[72],"being":[73],"due":[74],"fast":[77],"development":[78],"complexity":[83],"producing":[85],"representation":[87],"encompasses":[89],"all":[90],"structural":[91,140],"characteristics.":[94],"We":[95],"present":[96],"here":[97],"some":[98],"most":[101],"popular":[102],"electronic":[103],"molecular":[104],"macromolecular":[106],"used":[108],"many":[112],"which":[114],"are":[115,143],"based":[116],"on":[117,139,175],"graph":[118],"representations.":[119],"Furthermore,":[120],"we":[121],"describe":[122],"applications":[123,176],"these":[125,181],"AI-driven":[128],"discovery.":[130,152],"Our":[131],"aim":[132],"is":[133],"provide":[135],"brief":[137],"guide":[138,158],"essential":[144],"practice":[147],"AI":[149],"This":[153],"review":[154],"serves":[155],"as":[156],"for":[159],"researchers":[160],"who":[161],"little":[163],"experience":[164],"with":[165],"handling":[167],"plan":[172],"work":[174],"at":[177],"interface":[179]},"counts_by_year":[{"year":2026,"cited_by_count":40},{"year":2025,"cited_by_count":109},{"year":2024,"cited_by_count":136},{"year":2023,"cited_by_count":111},{"year":2022,"cited_by_count":94},{"year":2021,"cited_by_count":63},{"year":2020,"cited_by_count":4}],"updated_date":"2026-05-13T08:25:38.343686","created_date":"2025-10-10T00:00:00"}
