{"id":"https://openalex.org/W4386845335","doi":"https://doi.org/10.1021/acs.jcim.3c00667","title":"SILVR: Guided Diffusion for Molecule Generation","display_name":"SILVR: Guided Diffusion for Molecule Generation","publication_year":2023,"publication_date":"2023-09-19","ids":{"openalex":"https://openalex.org/W4386845335","doi":"https://doi.org/10.1021/acs.jcim.3c00667","pmid":"https://pubmed.ncbi.nlm.nih.gov/37724771"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c00667","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00667","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://doi.org/10.1021/acs.jcim.3c00667","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000143804","display_name":"Nicholas T. Runcie","orcid":null},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nicholas T. Runcie","raw_affiliation_strings":["EaSTCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, U.K"],"affiliations":[{"raw_affiliation_string":"EaSTCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, U.K","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004937381","display_name":"Antonia S. J. S. Mey","orcid":"https://orcid.org/0000-0001-7512-5252"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Antonia S.J.S. Mey","raw_affiliation_strings":["EaSTCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, U.K"],"affiliations":[{"raw_affiliation_string":"EaSTCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, U.K","institution_ids":["https://openalex.org/I98677209"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5004937381"],"corresponding_institution_ids":["https://openalex.org/I98677209"],"apc_list":null,"apc_paid":null,"fwci":5.486,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.96617989,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"63","issue":"19","first_page":"5996","last_page":"6005"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9951000213623047,"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":0.9951000213623047,"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":0.9894000291824341,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9731000065803528,"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/merge","display_name":"Merge (version control)","score":0.635985791683197},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5642133951187134},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.548437774181366},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.5308082103729248},{"id":"https://openalex.org/keywords/small-molecule","display_name":"Small molecule","score":0.507731556892395},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.4889739751815796},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.41694778203964233},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.41459327936172485},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3878972828388214},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.08054527640342712},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.07664698362350464}],"concepts":[{"id":"https://openalex.org/C197129107","wikidata":"https://www.wikidata.org/wiki/Q1921621","display_name":"Merge (version control)","level":2,"score":0.635985791683197},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5642133951187134},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.548437774181366},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.5308082103729248},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.507731556892395},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.4889739751815796},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.41694778203964233},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.41459327936172485},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3878972828388214},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08054527640342712},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.07664698362350464},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","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":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":true},{"descriptor_ui":"D000086782","descriptor_name":"Coronavirus 3C Proteases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000086782","descriptor_name":"Coronavirus 3C Proteases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1021/acs.jcim.3c00667","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00667","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:37724771","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37724771","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:10565820","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10565820","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10565820/pdf/ci3c00667.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"},{"id":"pmh:oai:pure.ed.ac.uk:openaire/15eb7654-a360-474c-9d4e-5a64acd52ebb","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/files/397879460/20230919MeyJCIMVoR.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400321","display_name":"Edinburgh Research Explorer (University of Edinburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98677209","host_organization_name":"University of Edinburgh","host_organization_lineage":["https://openalex.org/I98677209"],"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":"Runcie, N T & Mey, A S J S 2023, 'SILVR: Guided Diffusion for Molecule Generation', Journal of Chemical Information and Modeling, vol. 63, no. 19, pp. 5996-6005. https://doi.org/10.1021/acs.jcim.3c00667","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pure.ed.ac.uk:publications/15eb7654-a360-474c-9d4e-5a64acd52ebb","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/15eb7654-a360-474c-9d4e-5a64acd52ebb","pdf_url":null,"source":{"id":"https://openalex.org/S4306400321","display_name":"Edinburgh Research Explorer (University of Edinburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98677209","host_organization_name":"University of Edinburgh","host_organization_lineage":["https://openalex.org/I98677209"],"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":"Runcie, N T & Mey, A S J S 2023, 'SILVR: Guided Diffusion for Molecule Generation', Journal of Chemical Information and Modeling, vol. 63, no. 19, pp. 5996-6005. https://doi.org/10.1021/acs.jcim.3c00667","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.3c00667","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00667","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7200000286102295,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W2023818227","https://openalex.org/W2046258407","https://openalex.org/W2068672372","https://openalex.org/W2147122257","https://openalex.org/W2151971404","https://openalex.org/W2154777073","https://openalex.org/W2160592148","https://openalex.org/W2296575546","https://openalex.org/W2488106257","https://openalex.org/W2604272474","https://openalex.org/W2776451368","https://openalex.org/W2783658781","https://openalex.org/W2797324131","https://openalex.org/W2913668833","https://openalex.org/W2918813360","https://openalex.org/W3011847211","https://openalex.org/W3034806393","https://openalex.org/W3047663514","https://openalex.org/W3092125766","https://openalex.org/W3111206976","https://openalex.org/W3123775255","https://openalex.org/W3168686693","https://openalex.org/W3191805365","https://openalex.org/W3207414817","https://openalex.org/W3209764902","https://openalex.org/W4220798957","https://openalex.org/W4280562526","https://openalex.org/W4295996317","https://openalex.org/W4312497550","https://openalex.org/W4319072961","https://openalex.org/W4319164354","https://openalex.org/W4324129241","https://openalex.org/W4386804497","https://openalex.org/W6600225990","https://openalex.org/W6601728261"],"related_works":["https://openalex.org/W4365211920","https://openalex.org/W3014948380","https://openalex.org/W2043558654","https://openalex.org/W4380551139","https://openalex.org/W2280377497","https://openalex.org/W3174044702","https://openalex.org/W4238433571","https://openalex.org/W2967848559","https://openalex.org/W4283803360","https://openalex.org/W4317695495"],"abstract_inverted_index":{"Computationally":[0],"generating":[1],"new":[2,73,135,147,168],"synthetically":[3],"accessible":[4],"compounds":[5,35],"with":[6,190],"high":[7],"affinity":[8],"and":[9,123,193],"low":[10],"toxicity":[11],"is":[12,184],"a":[13,41,48,78,82,107,167],"great":[14],"challenge":[15],"in":[16,29],"drug":[17],"design.":[18],"Machine":[19],"learning":[20],"models":[21],"beyond":[22],"conventional":[23],"pharmacophoric":[24],"methods":[25],"have":[26],"shown":[27],"promise":[28],"the":[30,70,90,102,112,119,141,146,150,156,172,178],"generation":[31,71],"of":[32,72,81,101,121,137,155,174],"novel":[33],"small-molecule":[34],"but":[36],"require":[37],"significant":[38],"tuning":[39],"for":[40,57,110,197],"specific":[42],"protein":[43,83,188],"target.":[44],"Here,":[45],"we":[46,124],"introduce":[47],"method":[49,183],"called":[50],"selective":[51],"iterative":[52],"latent":[53],"variable":[54],"refinement":[55],"(SILVR)":[56],"conditioning":[58,111],"an":[59],"existing":[60],"diffusion-based":[61,195],"equivariant":[62],"generative":[63,180],"model":[64,68,196],"without":[65,153,170],"retraining.":[66],"The":[67,115],"allows":[69],"molecules":[74,136,148,175],"that":[75,98,126,145],"fit":[76,149],"into":[77,166],"binding":[79,151],"site":[80,152],"based":[84],"on":[85],"fragment":[86],"hits.":[87],"We":[88,158],"use":[89],"SARS-CoV-2":[91],"main":[92],"protease":[93],"fragments":[94,165,192],"from":[95],"Diamond":[96],"XChem":[97],"form":[99],"part":[100],"COVID":[103],"Moonshot":[104],"project":[105],"as":[106],"reference":[108],"dataset":[109],"molecule":[113,169,198],"generation.":[114,199],"SILVR":[116,128],"rate":[117],"controls":[118],"extent":[120],"conditioning,":[122],"show":[125],"moderate":[127],"rates":[129],"make":[130],"it":[131],"possible":[132],"to":[133,140,163,186],"generate":[134],"similar":[138],"shape":[139],"original":[142],"fragments,":[143],"meaning":[144],"knowledge":[154],"protein.":[157],"can":[159],"also":[160],"merge":[161],"up":[162],"3":[164],"affecting":[171],"quality":[173],"generated":[176],"by":[177],"underlying":[179],"model.":[181],"Our":[182],"generalizable":[185],"any":[187,194],"target":[189],"known":[191]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":10}],"updated_date":"2026-04-14T08:04:32.555800","created_date":"2025-10-10T00:00:00"}
