{"id":"https://openalex.org/W3186109768","doi":"https://doi.org/10.1021/acs.jcim.1c00561","title":"CHARMM-GUI <i>LBS Finder &amp; Refiner</i> for Ligand Binding Site Prediction and Refinement","display_name":"CHARMM-GUI <i>LBS Finder &amp; Refiner</i> for Ligand Binding Site Prediction and Refinement","publication_year":2021,"publication_date":"2021-07-23","ids":{"openalex":"https://openalex.org/W3186109768","doi":"https://doi.org/10.1021/acs.jcim.1c00561","mag":"3186109768","pmid":"https://pubmed.ncbi.nlm.nih.gov/34296608"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.1c00561","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00561","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":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8384712","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":"middle","author":{"id":"https://openalex.org/A5100690659","display_name":"Sang\u2010Jun Park","orcid":null},"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":"Sang-Jun Park","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/0000-0002-7307-3724","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":"middle","author":{"id":"https://openalex.org/A5100399317","display_name":"Han Zhang","orcid":"https://orcid.org/0000-0002-5608-9185"},"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":"Han Zhang","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/0000-0002-5608-9185","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":4,"corresponding_author_ids":["https://openalex.org/A5030884127"],"corresponding_institution_ids":["https://openalex.org/I186143895"],"apc_list":null,"apc_paid":null,"fwci":0.9771,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.74546567,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"61","issue":"8","first_page":"3744","last_page":"3751"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9995999932289124,"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"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9995999932289124,"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/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/T11162","display_name":"Enzyme Structure and Function","score":0.9945999979972839,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.7990779876708984},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7663550972938538},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.4804812967777252},{"id":"https://openalex.org/keywords/cartography","display_name":"Cartography","score":0.0730791687965393},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.062297672033309937}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7990779876708984},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7663550972938538},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.4804812967777252},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.0730791687965393},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.062297672033309937},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","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":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.1c00561","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00561","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:34296608","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34296608","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:8384712","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8384712","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:8384712","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8384712","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.4300000071525574,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G1976083906","display_name":null,"funder_award_id":"GM126140","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"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"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":79,"referenced_works":["https://openalex.org/W1508256447","https://openalex.org/W1966078827","https://openalex.org/W1968319881","https://openalex.org/W1969189143","https://openalex.org/W1971784203","https://openalex.org/W1976499671","https://openalex.org/W1983194490","https://openalex.org/W1990771438","https://openalex.org/W1998257485","https://openalex.org/W2020383072","https://openalex.org/W2021520922","https://openalex.org/W2026211752","https://openalex.org/W2030860488","https://openalex.org/W2031194866","https://openalex.org/W2031390939","https://openalex.org/W2037312364","https://openalex.org/W2050982038","https://openalex.org/W2058463742","https://openalex.org/W2064697628","https://openalex.org/W2069152576","https://openalex.org/W2073746700","https://openalex.org/W2077776336","https://openalex.org/W2090649877","https://openalex.org/W2091563009","https://openalex.org/W2111608447","https://openalex.org/W2115540209","https://openalex.org/W2118233996","https://openalex.org/W2125175309","https://openalex.org/W2126234813","https://openalex.org/W2127597332","https://openalex.org/W2127866370","https://openalex.org/W2128402268","https://openalex.org/W2130479394","https://openalex.org/W2132262459","https://openalex.org/W2139064989","https://openalex.org/W2140538197","https://openalex.org/W2144258433","https://openalex.org/W2145722722","https://openalex.org/W2146341019","https://openalex.org/W2158957954","https://openalex.org/W2159560083","https://openalex.org/W2161151688","https://openalex.org/W2164088236","https://openalex.org/W2168269595","https://openalex.org/W2200606379","https://openalex.org/W2206954826","https://openalex.org/W2300618309","https://openalex.org/W2335469959","https://openalex.org/W2346117320","https://openalex.org/W2405075761","https://openalex.org/W2468361502","https://openalex.org/W2474188283","https://openalex.org/W2515320816","https://openalex.org/W2607783486","https://openalex.org/W2612598385","https://openalex.org/W2617750324","https://openalex.org/W2623296956","https://openalex.org/W2767934754","https://openalex.org/W2795174361","https://openalex.org/W2807540482","https://openalex.org/W2887981960","https://openalex.org/W2905232362","https://openalex.org/W2913254604","https://openalex.org/W2913977622","https://openalex.org/W2914877211","https://openalex.org/W2914975766","https://openalex.org/W2949223833","https://openalex.org/W2951395093","https://openalex.org/W2955341169","https://openalex.org/W2976291065","https://openalex.org/W3007743886","https://openalex.org/W3013426051","https://openalex.org/W3042908073","https://openalex.org/W3046751266","https://openalex.org/W3096455667","https://openalex.org/W3114321016","https://openalex.org/W3119574697","https://openalex.org/W3129160401","https://openalex.org/W3199799076"],"related_works":["https://openalex.org/W1485630101","https://openalex.org/W2498017833","https://openalex.org/W2070338563","https://openalex.org/W112744582","https://openalex.org/W3081841992","https://openalex.org/W2030059621","https://openalex.org/W2081647779","https://openalex.org/W1490303524","https://openalex.org/W3033750096","https://openalex.org/W4234487584"],"abstract_inverted_index":{"A":[0],"protein":[1,33,166],"performs":[2],"its":[3,12],"task":[4],"by":[5,72],"binding":[6],"a":[7],"variety":[8],"of":[9,29,112,125,167],"ligands":[10],"in":[11,143],"local":[13,59],"region":[14],"that":[15,51,149],"is":[16,117,154],"also":[17],"known":[18],"as":[19,94],"the":[20],"ligand-binding-site":[21],"(LBS).":[22],"Therefore,":[23],"accurate":[24],"prediction,":[25],"characterization,":[26],"and":[27,36,63,70,99,123,128,139,159],"refinement":[28,104],"LBS":[30,46,60,79,82,102,113,120,136,150,162],"can":[31],"facilitate":[32],"functional":[34],"annotations":[35],"structure-based":[37],"drug":[38],"design.":[39],"In":[40],"this":[41],"work,":[42],"we":[43],"present":[44],"CHARMM-GUI":[45],"Finder":[47,83,114,151],"&":[48,84,115,152],"Refiner":[49,85,116,153],"(https://www.charmm-gui.org/input/lbsfinder)":[50],"predicts":[52],"potential":[53,161],"LBS,":[54],"offers":[55],"interactive":[56],"features":[57],"for":[58,78,101],"structure":[61,80,103,121,137],"analysis,":[62],"prepares":[64],"various":[65],"molecular":[66],"dynamics":[67],"(MD)":[68],"systems":[69],"inputs":[71],"setting":[73],"up":[74],"distance":[75],"restraint":[76],"potentials":[77],"refinement.":[81],"supports":[86],"5":[87],"different":[88],"commonly":[89],"used":[90],"simulation":[91],"programs,":[92],"such":[93],"NAMD,":[95],"AMBER,":[96],"GROMACS,":[97],"GENESIS,":[98],"OpenMM,":[100],"together":[105],"with":[106],"hydrogen":[107],"mass":[108],"repartitioning.":[109],"The":[110],"capability":[111],"illustrated":[118],"through":[119],"predictions":[122,138],"refinements":[124,140],"48":[126],"modeled":[127],"20":[129],"apo":[130],"benchmark":[131,145],"target":[132],"proteins.":[133],"Overall,":[134],"successful":[135],"are":[141],"seen":[142],"our":[144],"tests.":[146],"We":[147],"hope":[148],"useful":[155],"to":[156],"predict,":[157],"characterize,":[158],"refine":[160],"on":[163],"any":[164],"given":[165],"interest.":[168]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":1}],"updated_date":"2026-05-16T08:24:45.110214","created_date":"2021-08-02T00:00:00"}
