{"id":"https://openalex.org/W3107514001","doi":"https://doi.org/10.1021/acs.jcim.0c00767","title":"FragRep: A Web Server for Structure-Based Drug Design by Fragment Replacement","display_name":"FragRep: A Web Server for Structure-Based Drug Design by Fragment Replacement","publication_year":2020,"publication_date":"2020-12-04","ids":{"openalex":"https://openalex.org/W3107514001","doi":"https://doi.org/10.1021/acs.jcim.0c00767","mag":"3107514001","pmid":"https://pubmed.ncbi.nlm.nih.gov/33275427"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.0c00767","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00767","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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006440949","display_name":"Jinwen Shan","orcid":"https://orcid.org/0000-0001-8676-0438"},"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/I66867065","display_name":"East China Normal University","ror":"https://ror.org/02n96ep67","country_code":"CN","type":"education","lineage":["https://openalex.org/I66867065"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jinwen Shan","raw_affiliation_strings":["NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062 China","Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062 China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062 China","institution_ids":["https://openalex.org/I258800397"]},{"raw_affiliation_string":"Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062 China","institution_ids":["https://openalex.org/I66867065"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018141394","display_name":"Xiaolin Pan","orcid":"https://orcid.org/0000-0002-9465-3971"},"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/I66867065","display_name":"East China Normal University","ror":"https://ror.org/02n96ep67","country_code":"CN","type":"education","lineage":["https://openalex.org/I66867065"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaolin Pan","raw_affiliation_strings":["NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062 China","Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062 China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062 China","institution_ids":["https://openalex.org/I258800397"]},{"raw_affiliation_string":"Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062 China","institution_ids":["https://openalex.org/I66867065"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100351264","display_name":"Xingyu Wang","orcid":"https://orcid.org/0000-0002-0897-9933"},"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"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xingyu Wang","raw_affiliation_strings":["NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062 China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062 China","institution_ids":["https://openalex.org/I258800397"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110665338","display_name":"Xudong Xiao","orcid":null},"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/I66867065","display_name":"East China Normal University","ror":"https://ror.org/02n96ep67","country_code":"CN","type":"education","lineage":["https://openalex.org/I66867065"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xudong Xiao","raw_affiliation_strings":["NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062 China","Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062 China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062 China","institution_ids":["https://openalex.org/I258800397"]},{"raw_affiliation_string":"Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062 China","institution_ids":["https://openalex.org/I66867065"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077039256","display_name":"Changge Ji","orcid":"https://orcid.org/0000-0001-5477-4894"},"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/I66867065","display_name":"East China Normal University","ror":"https://ror.org/02n96ep67","country_code":"CN","type":"education","lineage":["https://openalex.org/I66867065"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Changge Ji","raw_affiliation_strings":["NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062 China","Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062 China"],"raw_orcid":"https://orcid.org/0000-0001-5477-4894","affiliations":[{"raw_affiliation_string":"NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062 China","institution_ids":["https://openalex.org/I258800397"]},{"raw_affiliation_string":"Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062 China","institution_ids":["https://openalex.org/I66867065"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5077039256"],"corresponding_institution_ids":["https://openalex.org/I258800397","https://openalex.org/I66867065"],"apc_list":null,"apc_paid":null,"fwci":2.3122,"has_fulltext":false,"cited_by_count":34,"citation_normalized_percentile":{"value":0.91071369,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"60","issue":"12","first_page":"5900","last_page":"5906"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"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":0.9998000264167786,"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":0.995199978351593,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9908999800682068,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/fragment","display_name":"Fragment (logic)","score":0.8219437599182129},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6775133609771729},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.6466888189315796},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.634235143661499},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.5662888288497925},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.4463575482368469},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.41066303849220276},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37477797269821167},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.35318657755851746},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2813236713409424},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.24088865518569946},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.23233652114868164},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.19051173329353333},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.17267394065856934},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12341633439064026},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.09036251902580261},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.06495079398155212}],"concepts":[{"id":"https://openalex.org/C2776235265","wikidata":"https://www.wikidata.org/wiki/Q18392052","display_name":"Fragment (logic)","level":2,"score":0.8219437599182129},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6775133609771729},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.6466888189315796},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.634235143661499},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5662888288497925},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.4463575482368469},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.41066303849220276},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37477797269821167},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.35318657755851746},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2813236713409424},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.24088865518569946},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.23233652114868164},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.19051173329353333},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.17267394065856934},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12341633439064026},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.09036251902580261},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.06495079398155212},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.0c00767","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00767","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:33275427","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33275427","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}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.550000011920929}],"awards":[{"id":"https://openalex.org/G427857027","display_name":null,"funder_award_id":"91753103","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6393484340","display_name":null,"funder_award_id":"2016YFA0501700","funder_id":"https://openalex.org/F4320321540","funder_display_name":"Ministry of Science and Technology of the People's Republic of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321540","display_name":"Ministry of Science and Technology of the People's Republic of China","ror":"https://ror.org/027s68j25"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1509196567","https://openalex.org/W1963607000","https://openalex.org/W1971947883","https://openalex.org/W1975743735","https://openalex.org/W1975875968","https://openalex.org/W1976203248","https://openalex.org/W1990724722","https://openalex.org/W2004408850","https://openalex.org/W2019048640","https://openalex.org/W2027423337","https://openalex.org/W2035162463","https://openalex.org/W2035349592","https://openalex.org/W2045629276","https://openalex.org/W2050273205","https://openalex.org/W2077703786","https://openalex.org/W2081852949","https://openalex.org/W2089248273","https://openalex.org/W2094120651","https://openalex.org/W2125624687","https://openalex.org/W2159593339","https://openalex.org/W2160592148","https://openalex.org/W2169678694","https://openalex.org/W2172242534","https://openalex.org/W2294932319","https://openalex.org/W2345719659","https://openalex.org/W2400204193","https://openalex.org/W2529996553","https://openalex.org/W2613042274","https://openalex.org/W2763694886","https://openalex.org/W2883435671","https://openalex.org/W2888438491","https://openalex.org/W2971116291","https://openalex.org/W2993893341","https://openalex.org/W3005002943","https://openalex.org/W3098269892"],"related_works":["https://openalex.org/W4319984742","https://openalex.org/W585106548","https://openalex.org/W2475765637","https://openalex.org/W2605185882","https://openalex.org/W2131900949","https://openalex.org/W2078653892","https://openalex.org/W3008041775","https://openalex.org/W4313463972","https://openalex.org/W2572080171","https://openalex.org/W2145118195"],"abstract_inverted_index":{"The":[0,32,59,109],"design":[1,9,28,100],"of":[2,73,77,98],"efficient":[3],"computational":[4,92],"tools":[5],"for":[6,12,25,94],"structure-guided":[7],"ligand":[8,27,39,79,99],"is":[10,34,89,112],"essential":[11],"the":[13,70,74,78,95],"drug":[14],"discovery":[15],"process.":[16],"We":[17],"hereby":[18],"present":[19],"FragRep,":[20],"a":[21,35,38,90],"new":[22],"web":[23],"server":[24,60],"structure-based":[26],"by":[29],"fragment":[30],"replacement.":[31],"input":[33],"protein":[36,43,86],"and":[37,117],"structure,":[40],"either":[41,102],"from":[42,47],"data":[44],"bank":[45],"or":[46,106],"molecular":[48],"docking.":[49],"Users":[50],"can":[51,118],"choose":[52],"specific":[53],"substructures":[54],"they":[55],"want":[56],"to":[57,62,115],"modify.":[58],"tries":[61],"find":[63],"suitable":[64],"fragments":[65],"that":[66],"not":[67],"only":[68],"meet":[69],"geometric":[71],"requirements":[72],"remaining":[75],"part":[76],"but":[80],"also":[81],"fit":[82],"well":[83],"with":[84],"local":[85],"environments.":[87],"FragRep":[88,110],"powerful":[91],"tool":[93],"rapid":[96],"generation":[97],"ideas;":[101],"in":[103],"scaffold":[104],"hopping":[105],"bioisosteric":[107],"replacing.":[108],"Server":[111],"freely":[113],"available":[114],"researchers":[116],"be":[119],"accessed":[120],"at":[121],"http://xundrug.cn/fragrep.":[122]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":7}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}