{"id":"https://openalex.org/W4306897068","doi":"https://doi.org/10.1021/acs.jcim.2c01079","title":"On Quality Thresholds for the Clustering of Molecular Structures","display_name":"On Quality Thresholds for the Clustering of Molecular Structures","publication_year":2022,"publication_date":"2022-10-20","ids":{"openalex":"https://openalex.org/W4306897068","doi":"https://doi.org/10.1021/acs.jcim.2c01079","pmid":"https://pubmed.ncbi.nlm.nih.gov/36264888"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c01079","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01079","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","license_id":"https://openalex.org/licenses/cc-by","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.2c01079","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027747641","display_name":"Xavier Daura","orcid":"https://orcid.org/0000-0001-9235-6730"},"institutions":[{"id":"https://openalex.org/I11932220","display_name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats","ror":"https://ror.org/0371hy230","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I11932220"]},{"id":"https://openalex.org/I123044942","display_name":"Universitat Aut\u00f2noma de Barcelona","ror":"https://ror.org/052g8jq94","country_code":"ES","type":"education","lineage":["https://openalex.org/I123044942"]},{"id":"https://openalex.org/I2801357902","display_name":"Instituto de Salud Carlos III","ror":"https://ror.org/00ca2c886","country_code":"ES","type":"funder","lineage":["https://openalex.org/I2801357902","https://openalex.org/I4387152914"]},{"id":"https://openalex.org/I4210105141","display_name":"Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine","ror":"https://ror.org/01gm5f004","country_code":"ES","type":"other","lineage":["https://openalex.org/I4210105141"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Xavier Daura","raw_affiliation_strings":["Catalan Institution for Research and Advanced Studies (ICREA), Barcelona08010, Spain","Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Bioingenier\u00eda, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Cerdanyola del Vall\u00e8s08193, Spain","Institute of Biotechnology and Biomedicine, Universitat Aut\u00f2noma de Barcelona, Cerdanyola del Vall\u00e8s08193, Spain"],"raw_orcid":"https://orcid.org/0000-0001-9235-6730","affiliations":[{"raw_affiliation_string":"Catalan Institution for Research and Advanced Studies (ICREA), Barcelona08010, Spain","institution_ids":["https://openalex.org/I11932220"]},{"raw_affiliation_string":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Bioingenier\u00eda, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Cerdanyola del Vall\u00e8s08193, Spain","institution_ids":["https://openalex.org/I2801357902","https://openalex.org/I4210105141"]},{"raw_affiliation_string":"Institute of Biotechnology and Biomedicine, Universitat Aut\u00f2noma de Barcelona, Cerdanyola del Vall\u00e8s08193, Spain","institution_ids":["https://openalex.org/I123044942"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001996210","display_name":"Oscar Conchillo\u2010Sol\u00e9","orcid":"https://orcid.org/0000-0003-4266-246X"},"institutions":[{"id":"https://openalex.org/I123044942","display_name":"Universitat Aut\u00f2noma de Barcelona","ror":"https://ror.org/052g8jq94","country_code":"ES","type":"education","lineage":["https://openalex.org/I123044942"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Oscar Conchillo-Sol\u00e9","raw_affiliation_strings":["Department of Genetics and Microbiology, Universitat Aut\u00f2noma de Barcelona, Cerdanyola del Vall\u00e8s08193, Spain","Institute of Biotechnology and Biomedicine, Universitat Aut\u00f2noma de Barcelona, Cerdanyola del Vall\u00e8s08193, Spain"],"raw_orcid":"https://orcid.org/0000-0003-4266-246X","affiliations":[{"raw_affiliation_string":"Department of Genetics and Microbiology, Universitat Aut\u00f2noma de Barcelona, Cerdanyola del Vall\u00e8s08193, Spain","institution_ids":["https://openalex.org/I123044942"]},{"raw_affiliation_string":"Institute of Biotechnology and Biomedicine, Universitat Aut\u00f2noma de Barcelona, Cerdanyola del Vall\u00e8s08193, Spain","institution_ids":["https://openalex.org/I123044942"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5027747641"],"corresponding_institution_ids":["https://openalex.org/I11932220","https://openalex.org/I123044942","https://openalex.org/I2801357902","https://openalex.org/I4210105141"],"apc_list":null,"apc_paid":null,"fwci":1.018,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.74360078,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"62","issue":"22","first_page":"5738","last_page":"5745"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9991999864578247,"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":0.9991999864578247,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9972000122070312,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9882000088691711,"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/cluster-analysis","display_name":"Cluster analysis","score":0.7961609363555908},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.624032199382782},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.597877562046051},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5807881951332092},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5407853126525879},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46755731105804443},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.4078250527381897},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3981491029262543},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2645264267921448},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.0843406617641449}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.7961609363555908},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.624032199382782},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.597877562046051},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5807881951332092},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5407853126525879},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46755731105804443},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.4078250527381897},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3981491029262543},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2645264267921448},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0843406617641449},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":4,"locations":[{"id":"doi:10.1021/acs.jcim.2c01079","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01079","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:36264888","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36264888","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:9709914","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9709914","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"},{"id":"pmh:oai:ddd.uab.cat:269351","is_oa":true,"landing_page_url":"https://ddd.uab.cat/record/269351","pdf_url":null,"source":{"id":"https://openalex.org/S4306400380","display_name":"Dip\u00f2sit Digital de Documents de la UAB (Universitat Aut\u00f2noma de Barcelona)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I123044942","host_organization_name":"Universitat Aut\u00f2noma de Barcelona","host_organization_lineage":["https://openalex.org/I123044942"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.2c01079","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01079","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","license_id":"https://openalex.org/licenses/cc-by","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/G3605207705","display_name":null,"funder_award_id":"PID2019-111364RB-I00","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"}],"funders":[{"id":"https://openalex.org/F4320322930","display_name":"Ministerio de Ciencia e Innovaci\u00f3n","ror":"https://ror.org/034900433"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":7,"referenced_works":["https://openalex.org/W1976208596","https://openalex.org/W2030728145","https://openalex.org/W2105321472","https://openalex.org/W2112878090","https://openalex.org/W2165779834","https://openalex.org/W2398670341","https://openalex.org/W2974711963"],"related_works":["https://openalex.org/W2487162673","https://openalex.org/W2942366970","https://openalex.org/W2793211469","https://openalex.org/W2949152769","https://openalex.org/W4372354731","https://openalex.org/W2562400057","https://openalex.org/W1692008701","https://openalex.org/W2597588799","https://openalex.org/W4360593462","https://openalex.org/W2894446834"],"abstract_inverted_index":{"It":[0],"has":[1,29],"been":[2,30],"recently":[3],"suggested":[4],"that":[5,135,176],"diametral":[6,165],"(so-called":[7],"quality)":[8],"similarity":[9,88],"thresholds":[10],"are":[11,148],"superior":[12],"to":[13,54,168],"radial":[14,163,203],"ones":[15],"for":[16,32,41,150,198],"the":[17,42,75,80,93,114,117,136,151,160,189,194],"clustering":[18,34,185],"of":[19,44,83,108,116],"molecular":[20,45,186],"three-dimensional":[21],"structures":[22,46,187],"(Gonz\u00e1lez-Alem\u00e1n":[23],"et":[24,56,63],"al.,":[25],"2020).":[26],"The":[27,154],"argument":[28],"made":[31,149],"two":[33,72,97,104,111,137],"algorithms":[35,73],"available":[36],"in":[37,110,170,204],"various":[38],"software":[39],"packages":[40],"analysis":[43],"from":[47,124],"ensembles":[48],"generated":[49],"by":[50],"computer":[51],"simulations,":[52],"attributed":[53],"Daura":[55],"al.":[57,64],"(1999)":[58,65],"(radial":[59],"threshold)":[60],"and":[61,99,113,130],"Heyer":[62],"(diametral":[66],"threshold).":[67],"Here,":[68],"we":[69],"compare":[70],"these":[71,96],"using":[74],"root-mean-squared":[76],"difference":[77],"(rmsd)":[78],"between":[79,95],"Cartesian":[81],"coordinates":[82,115],"selected":[84],"atoms":[85],"as":[86,143,145,191],"pairwise":[87],"metric.":[89],"We":[90,133,180],"discuss":[91],"formally":[92],"relation":[94],"methods":[98,138],"illustrate":[100],"their":[101],"behavior":[102],"with":[103,188],"examples,":[105],"a":[106,121,125,173,192,199],"set":[107],"points":[109],"dimensions":[112],"tau":[118],"polypeptide":[119],"along":[120],"trajectory":[122],"extracted":[123],"replica-exchange":[126],"molecular-dynamics":[127],"simulation":[128],"(Shea":[129],"Levine,":[131],"2016).":[132],"show":[134],"produce":[139],"equally":[140],"sized":[141],"clusters":[142],"long":[144],"adequate":[146],"choices":[147],"respective":[152],"thresholds.":[153],"real":[155],"issue":[156],"is":[157,162,177,201],"not":[158],"whether":[159],"threshold":[161,174,200],"or":[164],"but":[166],"how":[167],"choose":[169],"either":[171],"case":[172],"value":[175],"physically":[178],"meaningful.":[179],"will":[181],"argue":[182],"that,":[183],"when":[184],"rmsd":[190],"metric,":[193],"simplest":[195],"best":[196],"guess":[197],"actually":[202],"nature.":[205]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":5}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
