{"id":"https://openalex.org/W4213370488","doi":"https://doi.org/10.1093/bib/bbac087","title":"FitDock: protein\u2013ligand docking by template fitting","display_name":"FitDock: protein\u2013ligand docking by template fitting","publication_year":2022,"publication_date":"2022-02-21","ids":{"openalex":"https://openalex.org/W4213370488","doi":"https://doi.org/10.1093/bib/bbac087","pmid":"https://pubmed.ncbi.nlm.nih.gov/35289358"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac087","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac087","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5027864301","display_name":"Xiaocong Yang","orcid":"https://orcid.org/0000-0003-0027-3861"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaocong Yang","raw_affiliation_strings":["Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China"],"raw_orcid":"https://orcid.org/0000-0003-0027-3861","affiliations":[{"raw_affiliation_string":"Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088854393","display_name":"Yang Liu","orcid":"https://orcid.org/0000-0002-2517-9436"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Liu","raw_affiliation_strings":["Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China"],"raw_orcid":"https://orcid.org/0000-0002-2517-9436","affiliations":[{"raw_affiliation_string":"Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103212142","display_name":"Jianhong Gan","orcid":null},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianhong Gan","raw_affiliation_strings":["Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057608418","display_name":"Zhi\u2010Xiong Jim Xiao","orcid":"https://orcid.org/0000-0003-2504-5742"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhi-Xiong Xiao","raw_affiliation_strings":["Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045938742","display_name":"Yang Cao","orcid":"https://orcid.org/0000-0002-1925-2123"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]},{"id":"https://openalex.org/I4210165554","display_name":"Sichuan Center for Disease Control and Prevention","ror":"https://ror.org/05nda1d55","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210165554"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yang Cao","raw_affiliation_strings":["Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China","Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China"],"raw_orcid":"https://orcid.org/0000-0002-1925-2123","affiliations":[{"raw_affiliation_string":"Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China","institution_ids":["https://openalex.org/I4210165554"]},{"raw_affiliation_string":"Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I24185976"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5045938742"],"corresponding_institution_ids":["https://openalex.org/I24185976","https://openalex.org/I4210165554"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":35.3341,"has_fulltext":false,"cited_by_count":282,"citation_normalized_percentile":{"value":0.99857591,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"23","issue":"3","first_page":null,"last_page":null},"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9944999814033508,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9922999739646912,"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/docking","display_name":"Docking (animal)","score":0.7863184213638306},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.6150519251823425},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5915032029151917},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4758144021034241},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3494475483894348},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.30617302656173706},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19566971063613892},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1607387661933899},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.10528862476348877},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.07712388038635254},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.0741504430770874}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7863184213638306},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.6150519251823425},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5915032029151917},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4758144021034241},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3494475483894348},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.30617302656173706},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19566971063613892},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1607387661933899},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.10528862476348877},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.07712388038635254},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.0741504430770874},{"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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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:10.1093/bib/bbac087","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac087","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35289358","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35289358","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5598991704","display_name":null,"funder_award_id":"81973243","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W1484101819","https://openalex.org/W1605711358","https://openalex.org/W1983194490","https://openalex.org/W1985588649","https://openalex.org/W1993046136","https://openalex.org/W1999359666","https://openalex.org/W2013760445","https://openalex.org/W2019238324","https://openalex.org/W2022214219","https://openalex.org/W2028629022","https://openalex.org/W2048739031","https://openalex.org/W2050456292","https://openalex.org/W2051060071","https://openalex.org/W2052030759","https://openalex.org/W2056179306","https://openalex.org/W2058311929","https://openalex.org/W2059864723","https://openalex.org/W2068672372","https://openalex.org/W2070405735","https://openalex.org/W2070880994","https://openalex.org/W2072180710","https://openalex.org/W2072757166","https://openalex.org/W2084266282","https://openalex.org/W2094657212","https://openalex.org/W2102475066","https://openalex.org/W2110283222","https://openalex.org/W2114779636","https://openalex.org/W2123356345","https://openalex.org/W2130479394","https://openalex.org/W2131053638","https://openalex.org/W2134967712","https://openalex.org/W2136567909","https://openalex.org/W2142678478","https://openalex.org/W2143482176","https://openalex.org/W2145682943","https://openalex.org/W2154019529","https://openalex.org/W2158534713","https://openalex.org/W2169678694","https://openalex.org/W2178706210","https://openalex.org/W2222512263","https://openalex.org/W2296575546","https://openalex.org/W2301625241","https://openalex.org/W2789748145","https://openalex.org/W2886455199","https://openalex.org/W2910318997","https://openalex.org/W2954297401","https://openalex.org/W2955341169","https://openalex.org/W3030054993","https://openalex.org/W3105459299","https://openalex.org/W4200509818","https://openalex.org/W4230274588","https://openalex.org/W4293775970","https://openalex.org/W4296588184"],"related_works":["https://openalex.org/W1581147483","https://openalex.org/W4310018788","https://openalex.org/W4398796548","https://openalex.org/W2329052364","https://openalex.org/W2162967120","https://openalex.org/W1567411871","https://openalex.org/W2553094381","https://openalex.org/W2072180710","https://openalex.org/W2794807012","https://openalex.org/W2301625241"],"abstract_inverted_index":{"Protein-ligand":[0],"docking":[1,30,53,69,96,110,121],"is":[2,154],"an":[3,114],"essential":[4],"method":[5],"in":[6,107,135],"computer-aided":[7],"drug":[8,147],"design":[9,148],"and":[10,21,36,42,92,113,149],"structural":[11],"bioinformatics.":[12],"It":[13,153],"can":[14,49],"be":[15,50],"used":[16],"to":[17,52,77],"identify":[18],"active":[19],"compounds":[20],"reveal":[22],"molecular":[23,150],"mechanisms":[24],"of":[25,57,109,116],"biological":[26],"processes.":[27],"A":[28],"successful":[29],"usually":[31],"requires":[32],"thorough":[33],"conformation":[34,76],"sampling":[35],"scoring,":[37],"which":[38,73,139],"are":[39],"computationally":[40],"expensive":[41],"difficult.":[43],"Recent":[44],"studies":[45],"demonstrated":[46],"that":[47],"it":[48],"beneficial":[51],"with":[54],"the":[55,78,89],"guidance":[56],"existing":[58],"similar":[59],"co-crystal":[60],"structures.":[61],"In":[62,98],"this":[63],"work,":[64],"we":[65],"developed":[66],"a":[67,82,136,143],"protein-ligand":[68],"method,":[70],"named":[71],"FitDock,":[72],"fits":[74],"initial":[75],"given":[79],"template":[80,124],"using":[81],"hierarchical":[83],"multi-feature":[84],"alignment":[85],"approach,":[86],"subsequently":[87],"explores":[88],"possible":[90],"conformations":[91],"finally":[93],"outputs":[94],"refined":[95],"poses.":[97],"our":[99],"comprehensive":[100],"benchmark":[101],"tests,":[102],"FitDock":[103,131],"showed":[104],"40%-60%":[105],"improvement":[106],"terms":[108],"success":[111],"rate":[112],"order":[115],"magnitude":[117],"faster":[118],"over":[119],"popular":[120],"methods,":[122],"if":[123],"structures":[125],"exist":[126],"(>":[127],"0.5":[128],"ligand":[129],"similarity).":[130],"has":[132],"been":[133],"implemented":[134],"user-friendly":[137],"program,":[138],"could":[140],"serve":[141],"as":[142],"convenient":[144],"tool":[145],"for":[146,158],"mechanism":[151],"exploration.":[152],"now":[155],"freely":[156],"available":[157],"academic":[159],"users":[160],"at":[161],"http://cao.labshare.cn/fitdock/.":[162]},"counts_by_year":[{"year":2026,"cited_by_count":50},{"year":2025,"cited_by_count":117},{"year":2024,"cited_by_count":80},{"year":2023,"cited_by_count":28},{"year":2022,"cited_by_count":7}],"updated_date":"2026-05-13T08:25:38.343686","created_date":"2025-10-10T00:00:00"}
