{"id":"https://openalex.org/W4406271171","doi":"https://doi.org/10.1109/bibm62325.2024.10822743","title":"Advancing Template-Based Flexible Docking of P450-Heme Complexes via JAX MD","display_name":"Advancing Template-Based Flexible Docking of P450-Heme Complexes via JAX MD","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406271171","doi":"https://doi.org/10.1109/bibm62325.2024.10822743"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822743","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822743","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5001632689","display_name":"Rong Guo","orcid":"https://orcid.org/0000-0002-4005-5992"},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Rongxu Guo","raw_affiliation_strings":["Shandong University,School of Computer Science and Technology,Qingdao,China"],"affiliations":[{"raw_affiliation_string":"Shandong University,School of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I80143920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100420576","display_name":"Cheng Chen","orcid":"https://orcid.org/0000-0003-0384-6215"},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Cheng Chen","raw_affiliation_strings":["Shandong University,School of Computer Science and Technology,Qingdao,China"],"affiliations":[{"raw_affiliation_string":"Shandong University,School of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I80143920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114034179","display_name":"J. H. Sang","orcid":null},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiaheng Sang","raw_affiliation_strings":["Shandong University,School of Life Science,Qingdao,China"],"affiliations":[{"raw_affiliation_string":"Shandong University,School of Life Science,Qingdao,China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113115832","display_name":"Guishan Cui","orcid":null},"institutions":[{"id":"https://openalex.org/I1793135","display_name":"Yanbian University","ror":"https://ror.org/039xnh269","country_code":"CN","type":"education","lineage":["https://openalex.org/I1793135"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guishan Cui","raw_affiliation_strings":["Yanbian University,College of Geography and Ocean Sciences,China"],"affiliations":[{"raw_affiliation_string":"Yanbian University,College of Geography and Ocean Sciences,China","institution_ids":["https://openalex.org/I1793135"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100731978","display_name":"Fa Zhang","orcid":"https://orcid.org/0000-0002-2081-9369"},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fa Zhang","raw_affiliation_strings":["Beijing Institute of Technology,School of Medical Technology,Beijing,China"],"affiliations":[{"raw_affiliation_string":"Beijing Institute of Technology,School of Medical Technology,Beijing,China","institution_ids":["https://openalex.org/I125839683"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101906222","display_name":"Xuefeng Cui","orcid":"https://orcid.org/0000-0002-8816-3482"},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuefeng Cui","raw_affiliation_strings":["Shandong University,School of Computer Science and Technology,Qingdao,China"],"affiliations":[{"raw_affiliation_string":"Shandong University,School of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I80143920"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071932485","display_name":"Shengying Li","orcid":"https://orcid.org/0000-0002-5244-870X"},"institutions":[{"id":"https://openalex.org/I4391767886","display_name":"State Key Laboratory of Microbial Technology","ror":"https://ror.org/03x08qn04","country_code":null,"type":"facility","lineage":["https://openalex.org/I154099455","https://openalex.org/I4391767886"]},{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shengying Li","raw_affiliation_strings":["Shandong University,State Key Laboratory of Microbial Technology,Qingdao,China"],"affiliations":[{"raw_affiliation_string":"Shandong University,State Key Laboratory of Microbial Technology,Qingdao,China","institution_ids":["https://openalex.org/I154099455","https://openalex.org/I4391767886"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5001632689"],"corresponding_institution_ids":["https://openalex.org/I80143920"],"apc_list":null,"apc_paid":null,"fwci":0.196,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.52028568,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"675","last_page":"680"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11407","display_name":"Innovative Microfluidic and Catalytic Techniques Innovation","score":0.9700000286102295,"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"}},"topics":[{"id":"https://openalex.org/T11407","display_name":"Innovative Microfluidic and Catalytic Techniques Innovation","score":0.9700000286102295,"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"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9563000202178955,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.7416688799858093},{"id":"https://openalex.org/keywords/heme","display_name":"Heme","score":0.5822535157203674},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44521647691726685},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4290494918823242},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1051187515258789},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.07050657272338867}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7416688799858093},{"id":"https://openalex.org/C2776217839","wikidata":"https://www.wikidata.org/wiki/Q189621","display_name":"Heme","level":3,"score":0.5822535157203674},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44521647691726685},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4290494918823242},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1051187515258789},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.07050657272338867},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822743","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822743","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320337495","display_name":"Technology Development","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W2044028691","https://openalex.org/W2102245393","https://openalex.org/W2118233996","https://openalex.org/W2130479394","https://openalex.org/W2587418224","https://openalex.org/W2732184077","https://openalex.org/W2798194035","https://openalex.org/W2952578765","https://openalex.org/W3036082239","https://openalex.org/W3044938537","https://openalex.org/W3099810371","https://openalex.org/W3177828909","https://openalex.org/W3183475563","https://openalex.org/W3186179742","https://openalex.org/W4205948945","https://openalex.org/W4206488367","https://openalex.org/W4225637095","https://openalex.org/W4236236547","https://openalex.org/W4310058955","https://openalex.org/W4315646125","https://openalex.org/W4388819402","https://openalex.org/W4404755712","https://openalex.org/W6753420036","https://openalex.org/W6785566885"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2899084033","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487"],"abstract_inverted_index":{"AlphaFold2":[0],"has":[1,185],"advanced":[2],"protein":[3],"structure":[4,82],"prediction":[5],"but":[6],"often":[7],"overlooks":[8],"complexes":[9,39,183],"with":[10,160],"essential":[11],"ligands,":[12],"crucial":[13],"for":[14,101],"understanding":[15],"protein-ligand":[16,195],"interactions":[17],"relevant":[18],"to":[19,25,45,85,99,188],"drug":[20],"design.":[21],"AlphaFill":[22,136],"was":[23],"developed":[24,113],"integrate":[26],"ligands":[27],"and":[28,51,184,198],"ions":[29],"from":[30,168],"experimental":[31],"structures":[32],"into":[33],"predicted":[34,80],"models.":[35],"However,":[36],"many":[37],"resulting":[38],"lack":[40],"precise":[41],"spatial":[42,131],"constraints,":[43],"leading":[44],"clashes":[46],"between":[47],"filled":[48],"heme":[49],"atoms":[50,122],"the":[52,60,79,87,92,102,121,124,169,186],"P450":[53,81],"structure,":[54],"as":[55,57,83],"well":[56],"discrepancies":[58],"in":[59],"key":[61],"Fe-S":[62],"bond.So,":[63],"we":[64,95,112],"propose":[65],"FlexFill,":[66],"a":[67,114,145,191],"rapid":[68],"flexible":[69],"docking":[70,93],"algorithm":[71],"based":[72],"on":[73,120],"JAX":[74,97],"MD.":[75],"Specifically,":[76],"FlexFill":[77,143,154,176],"takes":[78],"input":[84],"generate":[86],"P450-heme":[88],"complex":[89],"structure.":[90],"During":[91],"process,":[94],"leverage":[96],"MD":[98],"account":[100],"structural":[103,140],"flexibility":[104],"of":[105,179,194],"P450.":[106],"Unlike":[107],"traditional":[108],"molecular":[109],"dynamics":[110],"methods,":[111],"customized":[115],"energy":[116],"function":[117],"that":[118,135,175],"focuses":[119],"near":[123],"pocket,":[125],"significantly":[126],"reducing":[127],"runtime":[128],"while":[129,142],"satisfying":[130],"constraints.The":[132],"results":[133],"indicate":[134],"experienced":[137],"almost":[138],"50%":[139],"crashes,":[141],"exhibited":[144],"substantially":[146],"lower":[147],"rate":[148],"at":[149,203],"less":[150],"than":[151,158],"5%.":[152],"Furthermore,":[153],"is":[155,177],"25%":[156],"faster":[157],"AlphaFill,":[159],"further":[161],"speed":[162],"improvements":[163],"by":[164],"removing":[165],"redundant":[166],"entries":[167],"template":[170],"library.":[171],"These":[172],"observations":[173],"suggest":[174],"capable":[178],"generating":[180],"high-fidelity":[181],"P450heme":[182],"ability":[187],"flexibly":[189],"dock":[190],"diverse":[192],"array":[193],"complexes.":[196],"Code":[197],"pre-trained":[199],"model":[200],"are":[201],"released":[202],"https://github.com/xfcui/FlexFill.":[204]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2025-12-22T23:10:17.713674","created_date":"2025-10-10T00:00:00"}
