{"id":"https://openalex.org/W4390582385","doi":"https://doi.org/10.1021/acs.jcim.3c01511","title":"Searching for Structure: Characterizing the Protein Conformational Landscape with Clustering-Based Algorithms","display_name":"Searching for Structure: Characterizing the Protein Conformational Landscape with Clustering-Based Algorithms","publication_year":2024,"publication_date":"2024-01-04","ids":{"openalex":"https://openalex.org/W4390582385","doi":"https://doi.org/10.1021/acs.jcim.3c01511","pmid":"https://pubmed.ncbi.nlm.nih.gov/38173388"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c01511","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01511","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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036659701","display_name":"Amanda C. Macke","orcid":"https://orcid.org/0000-0001-8927-0389"},"institutions":[{"id":"https://openalex.org/I63135867","display_name":"University of Cincinnati","ror":"https://ror.org/01e3m7079","country_code":"US","type":"education","lineage":["https://openalex.org/I63135867"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amanda C. Macke","raw_affiliation_strings":["Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States","institution_ids":["https://openalex.org/I63135867"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030826137","display_name":"Jacob E. Stump","orcid":"https://orcid.org/0000-0003-4080-2799"},"institutions":[{"id":"https://openalex.org/I63135867","display_name":"University of Cincinnati","ror":"https://ror.org/01e3m7079","country_code":"US","type":"education","lineage":["https://openalex.org/I63135867"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jacob E. Stump","raw_affiliation_strings":["Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States","institution_ids":["https://openalex.org/I63135867"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016314336","display_name":"Maria S. Kelly","orcid":"https://orcid.org/0009-0004-9266-5524"},"institutions":[{"id":"https://openalex.org/I63135867","display_name":"University of Cincinnati","ror":"https://ror.org/01e3m7079","country_code":"US","type":"education","lineage":["https://openalex.org/I63135867"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maria S. Kelly","raw_affiliation_strings":["Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States","institution_ids":["https://openalex.org/I63135867"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032770659","display_name":"Jamie Rowley","orcid":null},"institutions":[{"id":"https://openalex.org/I63135867","display_name":"University of Cincinnati","ror":"https://ror.org/01e3m7079","country_code":"US","type":"education","lineage":["https://openalex.org/I63135867"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jamie Rowley","raw_affiliation_strings":["Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States","institution_ids":["https://openalex.org/I63135867"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082837817","display_name":"Vageesha Herath","orcid":null},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]},{"id":"https://openalex.org/I63135867","display_name":"University of Cincinnati","ror":"https://ror.org/01e3m7079","country_code":"US","type":"education","lineage":["https://openalex.org/I63135867"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vageesha Herath","raw_affiliation_strings":["Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States","Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States","institution_ids":["https://openalex.org/I150468666"]},{"raw_affiliation_string":"Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States","institution_ids":["https://openalex.org/I63135867"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036013484","display_name":"Sarah Mullen","orcid":"https://orcid.org/0000-0002-7214-8763"},"institutions":[{"id":"https://openalex.org/I118746106","display_name":"College of Wooster","ror":"https://ror.org/029zqs055","country_code":"US","type":"education","lineage":["https://openalex.org/I118746106"]},{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sarah Mullen","raw_affiliation_strings":["Department of Chemistry, The College of Wooster, Wooster, Ohio 44691, United States","Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, The College of Wooster, Wooster, Ohio 44691, United States","institution_ids":["https://openalex.org/I118746106"]},{"raw_affiliation_string":"Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020568972","display_name":"Ruxandra I. Dima","orcid":"https://orcid.org/0000-0001-6105-7287"},"institutions":[{"id":"https://openalex.org/I63135867","display_name":"University of Cincinnati","ror":"https://ror.org/01e3m7079","country_code":"US","type":"education","lineage":["https://openalex.org/I63135867"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ruxandra I. Dima","raw_affiliation_strings":["Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States"],"raw_orcid":"https://orcid.org/0000-0001-6105-7287","affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States","institution_ids":["https://openalex.org/I63135867"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5020568972"],"corresponding_institution_ids":["https://openalex.org/I63135867"],"apc_list":null,"apc_paid":null,"fwci":1.0357,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.73893214,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"64","issue":"2","first_page":"470","last_page":"482"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":1.0,"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":1.0,"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":0.9939000010490417,"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"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9922000169754028,"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/cluster-analysis","display_name":"Cluster analysis","score":0.785402774810791},{"id":"https://openalex.org/keywords/dihedral-angle","display_name":"Dihedral angle","score":0.7765549421310425},{"id":"https://openalex.org/keywords/ramachandran-plot","display_name":"Ramachandran plot","score":0.7511452436447144},{"id":"https://openalex.org/keywords/maxima-and-minima","display_name":"Maxima and minima","score":0.7292227745056152},{"id":"https://openalex.org/keywords/globular-protein","display_name":"Globular protein","score":0.5172848701477051},{"id":"https://openalex.org/keywords/hierarchical-clustering","display_name":"Hierarchical clustering","score":0.503804624080658},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3875873386859894},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.38666847348213196},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3113945722579956},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.3052971065044403},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2800564765930176},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.26541852951049805},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2541157901287079},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2474379539489746},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.09218406677246094}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.785402774810791},{"id":"https://openalex.org/C89025888","wikidata":"https://www.wikidata.org/wiki/Q911907","display_name":"Dihedral angle","level":4,"score":0.7765549421310425},{"id":"https://openalex.org/C14301744","wikidata":"https://www.wikidata.org/wiki/Q579211","display_name":"Ramachandran plot","level":3,"score":0.7511452436447144},{"id":"https://openalex.org/C186633575","wikidata":"https://www.wikidata.org/wiki/Q845060","display_name":"Maxima and minima","level":2,"score":0.7292227745056152},{"id":"https://openalex.org/C105168689","wikidata":"https://www.wikidata.org/wiki/Q901969","display_name":"Globular protein","level":2,"score":0.5172848701477051},{"id":"https://openalex.org/C92835128","wikidata":"https://www.wikidata.org/wiki/Q1277447","display_name":"Hierarchical clustering","level":3,"score":0.503804624080658},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3875873386859894},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.38666847348213196},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3113945722579956},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3052971065044403},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2800564765930176},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.26541852951049805},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2541157901287079},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2474379539489746},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.09218406677246094},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.0},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D011487","descriptor_name":"Protein Conformation","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":"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},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064267","descriptor_name":"Intrinsically Disordered Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D064267","descriptor_name":"Intrinsically Disordered Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D064267","descriptor_name":"Intrinsically Disordered Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D064267","descriptor_name":"Intrinsically Disordered Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.3c01511","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01511","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:38173388","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38173388","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}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.5899999737739563,"display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G345480445","display_name":null,"funder_award_id":"CHE-1950244","funder_id":"https://openalex.org/F4320337393","funder_display_name":"Division of Chemistry"},{"id":"https://openalex.org/G7477931279","display_name":null,"funder_award_id":"1817948","funder_id":"https://openalex.org/F4320337397","funder_display_name":"Division of Molecular and Cellular Biosciences"}],"funders":[{"id":"https://openalex.org/F4320337393","display_name":"Division of Chemistry","ror":"https://ror.org/01ar8dr59"},{"id":"https://openalex.org/F4320337397","display_name":"Division of Molecular and Cellular Biosciences","ror":"https://ror.org/002jdaq33"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":81,"referenced_works":["https://openalex.org/W95014119","https://openalex.org/W1031578623","https://openalex.org/W1482971402","https://openalex.org/W1491824558","https://openalex.org/W1710827023","https://openalex.org/W1785817244","https://openalex.org/W1867464533","https://openalex.org/W1963819448","https://openalex.org/W1966078827","https://openalex.org/W1976295685","https://openalex.org/W1976499671","https://openalex.org/W1978562107","https://openalex.org/W1982251587","https://openalex.org/W1987971958","https://openalex.org/W1994840640","https://openalex.org/W1995816895","https://openalex.org/W2016170088","https://openalex.org/W2018540939","https://openalex.org/W2029667189","https://openalex.org/W2031043237","https://openalex.org/W2036755018","https://openalex.org/W2037788435","https://openalex.org/W2047962024","https://openalex.org/W2057477511","https://openalex.org/W2066158357","https://openalex.org/W2067174909","https://openalex.org/W2081693079","https://openalex.org/W2085487226","https://openalex.org/W2111249363","https://openalex.org/W2111397525","https://openalex.org/W2112878090","https://openalex.org/W2116695133","https://openalex.org/W2128572087","https://openalex.org/W2131793079","https://openalex.org/W2134099534","https://openalex.org/W2137322489","https://openalex.org/W2140992384","https://openalex.org/W2142529984","https://openalex.org/W2161605421","https://openalex.org/W2162785195","https://openalex.org/W2169693347","https://openalex.org/W2171268876","https://openalex.org/W2177944111","https://openalex.org/W2265874425","https://openalex.org/W2323178299","https://openalex.org/W2327524320","https://openalex.org/W2397148583","https://openalex.org/W2565914957","https://openalex.org/W2627044601","https://openalex.org/W2733722625","https://openalex.org/W2745147988","https://openalex.org/W2786733983","https://openalex.org/W2799870823","https://openalex.org/W2889129731","https://openalex.org/W2892940574","https://openalex.org/W2898466285","https://openalex.org/W2924564326","https://openalex.org/W2939121840","https://openalex.org/W2953016572","https://openalex.org/W2953107349","https://openalex.org/W2982926407","https://openalex.org/W3003257820","https://openalex.org/W3007953280","https://openalex.org/W3083406432","https://openalex.org/W3091498413","https://openalex.org/W3100278803","https://openalex.org/W3110435694","https://openalex.org/W3131653660","https://openalex.org/W3176792793","https://openalex.org/W3177828909","https://openalex.org/W3195375135","https://openalex.org/W3198047987","https://openalex.org/W3211795435","https://openalex.org/W4211196614","https://openalex.org/W4225655998","https://openalex.org/W4282942954","https://openalex.org/W4284990061","https://openalex.org/W4297236293","https://openalex.org/W4306897068","https://openalex.org/W4312113976","https://openalex.org/W4320040108"],"related_works":["https://openalex.org/W2111979569","https://openalex.org/W2047962024","https://openalex.org/W2169379013","https://openalex.org/W4317935117","https://openalex.org/W5642939","https://openalex.org/W2000232506","https://openalex.org/W2164993354","https://openalex.org/W1600511639","https://openalex.org/W4295897800","https://openalex.org/W2222296774"],"abstract_inverted_index":{"The":[0,70],"identification":[1,100],"and":[2,15,46,54,133,153,198,245],"characterization":[3],"of":[4,24,58,67,72,77,93,101,105,116,130,150,160,166,171,195,218,224],"the":[5,22,25,41,44,55,59,64,78,84,90,94,99,102,106,114,119,140,151,189,196,203,206,211,225,240],"main":[6,103],"conformations":[7,161],"from":[8,83,162,180,205,247],"a":[9,13,51,181,215],"protein":[10,37,52,68,131,175],"population":[11],"are":[12],"challenging":[14],"inherently":[16],"high-dimensional":[17],"problem.":[18],"Here,":[19],"we":[20,184],"evaluate":[21],"performance":[23,115],"Secondary":[26],"sTructural":[27],"Ensembles":[28],"with":[29,118,134],"machine":[30],"LeArning":[31],"(StELa)":[32],"double-clustering":[33],"method,":[34],"which":[35,125],"clusters":[36,219],"structures":[38,132],"based":[39,147],"on":[40,63,127,148],"relationship":[42],"between":[43,232],"\u03c6":[45,152],"\u03c8":[47,154],"dihedral":[48,155],"angles":[49],"in":[50],"backbone":[53],"secondary":[56],"structure":[57,144],"protein,":[60,183],"thus":[61,227],"focusing":[62],"local":[65],"properties":[66,129],"structures.":[69],"classification":[71],"states":[73,201],"as":[74],"vectors":[75,95],"composed":[76],"clusters'":[79],"indices":[80],"arising":[81],"naturally":[82],"Ramachandran":[85],"plot":[86],"is":[87,188],"followed":[88],"by":[89],"hierarchical":[91],"clustering":[92,123,145,190],"to":[96,230],"allow":[97],"for":[98,242],"features":[104],"corresponding":[107,207],"free":[108],"energy":[109,200],"landscape":[110],"(FEL).":[111],"We":[112],"compare":[113],"StELa":[117,187],"established":[120],"root-mean-squared-deviation":[121],"(RMSD)-based":[122],"algorithm,":[124],"focuses":[126],"global":[128],"Combinatorial":[135],"Averaged":[136],"Transient":[137],"Structure":[138],"(CATS),":[139],"combinatorial":[141],"averaged":[142],"transient":[143],"method":[146,191],"distributions":[149],"angle":[156],"coordinates.":[157],"Using":[158],"ensembles":[159],"molecular":[163],"dynamics":[164],"simulations":[165],"intrinsically":[167],"disordered":[168],"proteins":[169],"(IDPs)":[170],"various":[172],"lengths":[173],"(tau":[174],"fragments)":[176],"or":[177],"short":[178],"fragments":[179,246],"globular":[182,248],"show":[185],"that":[186,192,220],"identifies":[193],"many":[194],"minima":[197,204],"relevant":[199],"around":[202],"FELs.":[208],"In":[209],"contrast,":[210],"RMSD-based":[212],"algorithm":[213],"yields":[214],"large":[216],"number":[217],"usually":[221],"cover":[222],"most":[223],"FEL,":[226],"being":[228],"unable":[229],"distinguish":[231],"states,":[233],"while":[234],"CATS":[235],"does":[236],"not":[237],"sample":[238],"well":[239],"FELs":[241],"long":[243],"IDPs":[244],"proteins.":[249]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-03T09:05:47.796612","created_date":"2025-10-10T00:00:00"}