{"id":"https://openalex.org/W4384626471","doi":"https://doi.org/10.1021/acs.jcim.3c00416","title":"CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein\u2013Ligand Binding Modes","display_name":"CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein\u2013Ligand Binding Modes","publication_year":2023,"publication_date":"2023-07-18","ids":{"openalex":"https://openalex.org/W4384626471","doi":"https://doi.org/10.1021/acs.jcim.3c00416","pmid":"https://pubmed.ncbi.nlm.nih.gov/37462607"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c00416","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00416","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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.3c00416","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034984173","display_name":"Hugo Guterres","orcid":"https://orcid.org/0000-0001-7683-8385"},"institutions":[{"id":"https://openalex.org/I186143895","display_name":"Lehigh University","ror":"https://ror.org/012afjb06","country_code":"US","type":"education","lineage":["https://openalex.org/I186143895"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hugo Guterres","raw_affiliation_strings":["Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States"],"raw_orcid":"https://orcid.org/0000-0001-7683-8385","affiliations":[{"raw_affiliation_string":"Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States","institution_ids":["https://openalex.org/I186143895"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030884127","display_name":"Wonpil Im","orcid":"https://orcid.org/0000-0001-5642-6041"},"institutions":[{"id":"https://openalex.org/I186143895","display_name":"Lehigh University","ror":"https://ror.org/012afjb06","country_code":"US","type":"education","lineage":["https://openalex.org/I186143895"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Wonpil Im","raw_affiliation_strings":["Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States"],"raw_orcid":"https://orcid.org/0000-0001-5642-6041","affiliations":[{"raw_affiliation_string":"Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States","institution_ids":["https://openalex.org/I186143895"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5030884127"],"corresponding_institution_ids":["https://openalex.org/I186143895"],"apc_list":null,"apc_paid":null,"fwci":4.6512,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.95743831,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"63","issue":"15","first_page":"4772","last_page":"4779"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9973000288009644,"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/T11663","display_name":"Viral Infectious Diseases and Gene Expression in Insects","score":0.9718999862670898,"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":0.7764450311660767},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7232077121734619},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.704688310623169},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5987789630889893},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4067358672618866},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3949769139289856},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.2744842767715454},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.1855790913105011},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.15581351518630981},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.13582077622413635},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11135032773017883},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.05879020690917969}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7764450311660767},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7232077121734619},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.704688310623169},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5987789630889893},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4067358672618866},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3949769139289856},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.2744842767715454},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.1855790913105011},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.15581351518630981},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.13582077622413635},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11135032773017883},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.05879020690917969},{"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":"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":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","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":3,"locations":[{"id":"doi:10.1021/acs.jcim.3c00416","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00416","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:37462607","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37462607","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:10428204","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10428204","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10428204/pdf/ci3c00416.pdf","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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.3c00416","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00416","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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/G7700811841","display_name":null,"funder_award_id":"GM138472","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8085437342","display_name":null,"funder_award_id":"GM138472","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W1508256447","https://openalex.org/W1881444267","https://openalex.org/W1966078827","https://openalex.org/W1968562507","https://openalex.org/W1969189143","https://openalex.org/W1971062326","https://openalex.org/W1975945758","https://openalex.org/W1994782559","https://openalex.org/W2010004274","https://openalex.org/W2019732485","https://openalex.org/W2021520922","https://openalex.org/W2024704410","https://openalex.org/W2026211752","https://openalex.org/W2035687084","https://openalex.org/W2050982038","https://openalex.org/W2070753604","https://openalex.org/W2118233996","https://openalex.org/W2120988271","https://openalex.org/W2134967712","https://openalex.org/W2145722722","https://openalex.org/W2147993766","https://openalex.org/W2162967120","https://openalex.org/W2206954826","https://openalex.org/W2271736303","https://openalex.org/W2334483166","https://openalex.org/W2335469959","https://openalex.org/W2555870966","https://openalex.org/W2564298127","https://openalex.org/W2607783486","https://openalex.org/W2800892557","https://openalex.org/W2913359477","https://openalex.org/W2914975766","https://openalex.org/W2949223833","https://openalex.org/W2955998834","https://openalex.org/W2976291065","https://openalex.org/W3017113448","https://openalex.org/W3042908073","https://openalex.org/W3046751266","https://openalex.org/W3109230444","https://openalex.org/W3114321016","https://openalex.org/W3119574697","https://openalex.org/W3151633358","https://openalex.org/W3186109768","https://openalex.org/W3209921099","https://openalex.org/W4291214694","https://openalex.org/W4293364222","https://openalex.org/W4296327630","https://openalex.org/W4308370544","https://openalex.org/W4377091560"],"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":{"Molecular":[0],"docking":[1,35,81],"is":[2,20,30],"a":[3,31,76,148],"preferred":[4],"method":[5],"to":[6,15,40,57,84,196],"predict":[7],"ligand":[8,55,131,199],"binding":[9,13,47,56,60,88,98,135,145,200],"modes":[10,201],"and":[11,71,110,137],"their":[12],"energy":[14],"target":[16,159],"protein":[17],"receptors,":[18],"which":[19],"critical":[21],"in":[22,34,121],"early":[23],"phase":[24],"structure-based":[25],"drug":[26],"discovery.":[27],"However,":[28],"there":[29],"persistent":[32],"challenge":[33],"that":[36,189],"can":[37,193],"be":[38,194],"attributed":[39],"the":[41,130,138,162,184,190],"induced":[42,50,79],"fit":[43,51,80],"effect,":[44],"as":[45],"receptor":[46,97,108],"sites":[48],"undergo":[49],"conformational":[52],"changes":[53],"upon":[54],"achieve":[58],"better":[59],"modes.":[61,89],"In":[62],"this":[63,172],"work,":[64],"based":[65,128],"on":[66,129,171],"CHARMM-GUI":[67,78],"LBS":[68],"Finder&":[69],"Refiner":[70],"High-Throughput":[72],"Simulator,":[73],"we":[74,151],"present":[75],"straightforward":[77],"(CGUI-IFD)":[82],"workflow":[83,92,192],"generate":[85,197],"reliable":[86,198],"protein\u2013ligand":[87,118,155],"The":[90,124,167],"CGUI-IFD":[91,170,191],"generates":[93],"an":[94],"ensemble":[95],"of":[96,117,169],"site":[99,103],"conformations":[100],"through":[101],"ligand-binding":[102],"(LBS)":[104],"refinement,":[105],"runs":[106],"rigid":[107],"docking,":[109],"performs":[111],"high-throughput":[112],"molecular":[113,139],"dynamics":[114],"(MD)":[115],"simulations":[116],"complex":[119],"structures":[120],"explicit":[122],"solvents.":[123],"results":[125],"are":[126],"evaluated":[127],"root-mean-square":[132],"deviation":[133],"(RMSD)-based":[134],"stability":[136],"mechanics":[140],"generalized":[141],"Born":[142],"surface":[143],"area":[144],"energy.":[146],"For":[147],"benchmark":[149],"test,":[150],"used":[152],"258":[153],"cross-docking":[154,203],"pairs":[156],"across":[157],"41":[158],"proteins":[160],"from":[161,183],"Schrodinger":[163],"IFD-MD":[164],"data":[165,173],"set.":[166],"application":[168],"set":[174],"shows":[175],"80%":[176],"success":[177],"rate":[178],"(within":[179],"2.5":[180],"\u00c5":[181],"RMSD":[182],"experimental":[185],"structures).":[186],"We":[187],"expect":[188],"useful":[195],"for":[202],"cases.":[204]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":7}],"updated_date":"2026-06-12T08:23:45.883708","created_date":"2025-10-10T00:00:00"}
