{"id":"https://openalex.org/W3164973443","doi":"https://doi.org/10.1021/acs.jcim.1c00103","title":"DeepFrag: An Open-Source Browser App for Deep-Learning Lead Optimization","display_name":"DeepFrag: An Open-Source Browser App for Deep-Learning Lead Optimization","publication_year":2021,"publication_date":"2021-05-24","ids":{"openalex":"https://openalex.org/W3164973443","doi":"https://doi.org/10.1021/acs.jcim.1c00103","mag":"3164973443","pmid":"https://pubmed.ncbi.nlm.nih.gov/34029094"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.1c00103","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00103","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.1c00103","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":"bronze","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.1c00103","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021567178","display_name":"Harrison Green","orcid":"https://orcid.org/0000-0003-3986-3906"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Harrison Green","raw_affiliation_strings":["Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084976210","display_name":"Jacob D. Durrant","orcid":"https://orcid.org/0000-0002-5808-4097"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jacob D. Durrant","raw_affiliation_strings":["Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States"],"raw_orcid":"https://orcid.org/0000-0002-5808-4097","affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States","institution_ids":["https://openalex.org/I170201317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5084976210"],"corresponding_institution_ids":["https://openalex.org/I170201317"],"apc_list":null,"apc_paid":null,"fwci":4.2612,"has_fulltext":false,"cited_by_count":39,"citation_normalized_percentile":{"value":0.94672404,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"61","issue":"6","first_page":"2523","last_page":"2529"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9994999766349792,"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":0.9994999766349792,"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":0.9980999827384949,"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/T11407","display_name":"Innovative Microfluidic and Catalytic Techniques Innovation","score":0.9973000288009644,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8039830327033997},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7906477451324463},{"id":"https://openalex.org/keywords/upload","display_name":"Upload","score":0.7685668468475342},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6265656352043152},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.6003572344779968},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.5305037498474121},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.5282805562019348},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.4745793342590332},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4514082074165344},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.42943310737609863},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.25053098797798157},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.22549572587013245}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8039830327033997},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7906477451324463},{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.7685668468475342},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6265656352043152},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.6003572344779968},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.5305037498474121},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.5282805562019348},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.4745793342590332},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4514082074165344},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.42943310737609863},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.25053098797798157},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.22549572587013245},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","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":"D006801","descriptor_name":"Humans","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063731","descriptor_name":"Mobile Applications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063731","descriptor_name":"Mobile Applications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063731","descriptor_name":"Mobile Applications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063731","descriptor_name":"Mobile Applications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064878","descriptor_name":"Web Browser","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.1c00103","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00103","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.1c00103","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:34029094","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34029094","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:8243318","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8243318","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.1c00103","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00103","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.1c00103","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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5481392483","display_name":null,"funder_award_id":"R01GM132353","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":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3164973443.pdf","grobid_xml":"https://content.openalex.org/works/W3164973443.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1978159078","https://openalex.org/W2026498605","https://openalex.org/W2030596305","https://openalex.org/W2033016300","https://openalex.org/W2043592573","https://openalex.org/W2101368370","https://openalex.org/W2112120587","https://openalex.org/W2116142935","https://openalex.org/W2118571345","https://openalex.org/W2140047797","https://openalex.org/W2146465875","https://openalex.org/W2162415170","https://openalex.org/W2779144909","https://openalex.org/W2902625972","https://openalex.org/W2951019917","https://openalex.org/W2982398814","https://openalex.org/W3019731380","https://openalex.org/W3024423177","https://openalex.org/W3036674808","https://openalex.org/W3119225668","https://openalex.org/W3161725201","https://openalex.org/W4229658977","https://openalex.org/W4234985631"],"related_works":["https://openalex.org/W3034716491","https://openalex.org/W4240625990","https://openalex.org/W4401741136","https://openalex.org/W2557718140","https://openalex.org/W4386470600","https://openalex.org/W4399490472","https://openalex.org/W67092138","https://openalex.org/W2789551765","https://openalex.org/W2367815957","https://openalex.org/W2113128227"],"abstract_inverted_index":{"Lead":[0],"optimization,":[1],"a":[2,15,29,38,51,70,97,119],"critical":[3],"step":[4],"in":[5,46,80],"early":[6],"stage":[7],"drug":[8],"discovery,":[9],"involves":[10],"making":[11],"chemical":[12],"modifications":[13],"to":[14,18,91,96],"small-molecule":[16],"ligand":[17],"improve":[19],"properties":[20],"such":[21,35],"as":[22],"binding":[23],"affinity.":[24],"We":[25,111],"recently":[26],"developed":[27],"DeepFrag,":[28],"deep-learning":[30],"model":[31,79],"capable":[32],"of":[33,54,107,132,150],"recommending":[34],"modifications.":[36],"Though":[37],"powerful":[39],"hypothesis-generating":[40],"tool,":[41],"DeepFrag":[42,65,78],"is":[43,141],"currently":[44],"implemented":[45],"Python":[47],"and":[48,125],"so":[49],"requires":[50],"certain":[52],"degree":[53],"computational":[55],"expertise.":[56],"To":[57],"encourage":[58],"broader":[59],"adoption,":[60],"we":[61],"have":[62],"created":[63],"the":[64,77,104,115,148,151],"browser":[66,85],"app,":[67],"which":[68],"provides":[69],"user-friendly":[71],"graphical":[72],"user":[73],"interface":[74],"that":[75,114],"runs":[76],"users'":[81],"web":[82],"browsers.":[83],"The":[84,138],"app":[86,116],"does":[87,101],"not":[88],"require":[89,103],"users":[90],"upload":[92],"their":[93],"molecular":[94],"structures":[95],"third-party":[98,109],"server,":[99],"nor":[100],"it":[102],"separate":[105],"installation":[106],"any":[108],"software.":[110],"are":[112],"hopeful":[113],"will":[117],"be":[118,129],"useful":[120],"tool":[121],"for":[122],"both":[123],"researchers":[124],"students.":[126],"It":[127],"can":[128],"accessed":[130],"free":[131],"charge,":[133],"without":[134],"registration,":[135],"at":[136,144],"http://durrantlab.com/deepfrag.":[137],"source":[139],"code":[140],"also":[142],"available":[143],"http://git.durrantlab.com/jdurrant/deepfrag-app,":[145],"released":[146],"under":[147],"terms":[149],"open-source":[152],"Apache":[153],"License,":[154],"Version":[155],"2.0.":[156]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":4}],"updated_date":"2026-05-05T08:41:31.759640","created_date":"2025-10-10T00:00:00"}
