{"id":"https://openalex.org/W2969305656","doi":"https://doi.org/10.1021/acs.jcim.9b00215","title":"Systematic Exploration of Protein Conformational Space Using a Distance Geometry Approach","display_name":"Systematic Exploration of Protein Conformational Space Using a Distance Geometry Approach","publication_year":2019,"publication_date":"2019-08-23","ids":{"openalex":"https://openalex.org/W2969305656","doi":"https://doi.org/10.1021/acs.jcim.9b00215","mag":"2969305656","pmid":"https://pubmed.ncbi.nlm.nih.gov/31442036"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b00215","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00215","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://hal.science/hal-02350285","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048175686","display_name":"Th\u00e9r\u00e8se E. Malliavin","orcid":"https://orcid.org/0000-0002-3276-3366"},"institutions":[{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Th\u00e9r\u00e8se E. Malliavin","raw_affiliation_strings":["Unit\u00e9 de Bioinformatique Structurale, UMR 3528, CNRS, and Departement de Bioinformatique, Biostatistique et Biologie Int\u00e9grative, USR 3756, CNRS, Institut Pasteur, 75015 Paris, France"],"affiliations":[{"raw_affiliation_string":"Unit\u00e9 de Bioinformatique Structurale, UMR 3528, CNRS, and Departement de Bioinformatique, Biostatistique et Biologie Int\u00e9grative, USR 3756, CNRS, Institut Pasteur, 75015 Paris, France","institution_ids":["https://openalex.org/I157536573","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049200982","display_name":"Antonio Mucherino","orcid":"https://orcid.org/0000-0003-1824-3724"},"institutions":[{"id":"https://openalex.org/I2802519937","display_name":"Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires","ror":"https://ror.org/00myn0z94","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210159245","https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Antonio Mucherino","raw_affiliation_strings":["IRISA, 35042 Rennes, France"],"affiliations":[{"raw_affiliation_string":"IRISA, 35042 Rennes, France","institution_ids":["https://openalex.org/I2802519937"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076792725","display_name":"Carlile Lavor","orcid":"https://orcid.org/0000-0002-8105-3627"},"institutions":[{"id":"https://openalex.org/I181391015","display_name":"Universidade Estadual de Campinas (UNICAMP)","ror":"https://ror.org/04wffgt70","country_code":"BR","type":"education","lineage":["https://openalex.org/I181391015"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Carlile Lavor","raw_affiliation_strings":["Applied Math Department, IMECC\u2212University of Campinas, Campinas, SP 13083-970, Brazil"],"affiliations":[{"raw_affiliation_string":"Applied Math Department, IMECC\u2212University of Campinas, Campinas, SP 13083-970, Brazil","institution_ids":["https://openalex.org/I181391015"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046138085","display_name":"Leo Liberti","orcid":"https://orcid.org/0000-0003-3139-6821"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Leo Liberti","raw_affiliation_strings":["LIX CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, Route de Saclay, 91128 Palaiseau, France"],"affiliations":[{"raw_affiliation_string":"LIX CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, Route de Saclay, 91128 Palaiseau, France","institution_ids":["https://openalex.org/I142476485","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5046138085","https://openalex.org/A5048175686"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I142476485","https://openalex.org/I157536573"],"apc_list":null,"apc_paid":null,"fwci":1.9604,"has_fulltext":false,"cited_by_count":36,"citation_normalized_percentile":{"value":0.86934288,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"59","issue":"10","first_page":"4486","last_page":"4503"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9988999962806702,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9980999827384949,"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/dihedral-angle","display_name":"Dihedral angle","score":0.6775025725364685},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5833468437194824},{"id":"https://openalex.org/keywords/interval","display_name":"Interval (graph theory)","score":0.5413373112678528},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.519846498966217},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.4894162714481354},{"id":"https://openalex.org/keywords/convergence","display_name":"Convergence (economics)","score":0.47958341240882874},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4715076982975006},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.42782971262931824},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.40747570991516113},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.37256765365600586},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.29184025526046753},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.16056156158447266},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.08649307489395142}],"concepts":[{"id":"https://openalex.org/C89025888","wikidata":"https://www.wikidata.org/wiki/Q911907","display_name":"Dihedral angle","level":4,"score":0.6775025725364685},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5833468437194824},{"id":"https://openalex.org/C2778067643","wikidata":"https://www.wikidata.org/wiki/Q166507","display_name":"Interval (graph theory)","level":2,"score":0.5413373112678528},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.519846498966217},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.4894162714481354},{"id":"https://openalex.org/C2777303404","wikidata":"https://www.wikidata.org/wiki/Q759757","display_name":"Convergence (economics)","level":2,"score":0.47958341240882874},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4715076982975006},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.42782971262931824},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.40747570991516113},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.37256765365600586},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.29184025526046753},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.16056156158447266},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.08649307489395142},{"id":"https://openalex.org/C50522688","wikidata":"https://www.wikidata.org/wiki/Q189833","display_name":"Economic growth","level":1,"score":0.0},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"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":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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jcim.9b00215","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00215","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:31442036","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31442036","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:HAL:hal-02350285v1","is_oa":true,"landing_page_url":"https://hal.science/hal-02350285","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Chemical Information and Modeling, 2019, 59 (10), pp.4486-4503. &#x27E8;10.1021/acs.jcim.9b00215&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:HAL:pasteur-02330040v1","is_oa":false,"landing_page_url":"https://hal-pasteur.archives-ouvertes.fr/pasteur-02330040","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1549-9596","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:HAL:hal-02350285v1","is_oa":true,"landing_page_url":"https://hal.science/hal-02350285","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Chemical Information and Modeling, 2019, 59 (10), pp.4486-4503. &#x27E8;10.1021/acs.jcim.9b00215&#x27E9;","raw_type":"Journal articles"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320307044","display_name":"Pasteur Foundation","ror":"https://ror.org/01n0cq521"},{"id":"https://openalex.org/F4320320997","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","ror":"https://ror.org/02ddkpn78"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"},{"id":"https://openalex.org/F4320322141","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12"},{"id":"https://openalex.org/F4320322892","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":90,"referenced_works":["https://openalex.org/W65738273","https://openalex.org/W199186236","https://openalex.org/W635573473","https://openalex.org/W1522341432","https://openalex.org/W1590020374","https://openalex.org/W1674342371","https://openalex.org/W1773478864","https://openalex.org/W1908489692","https://openalex.org/W1970594638","https://openalex.org/W1972865089","https://openalex.org/W1973255639","https://openalex.org/W1979915001","https://openalex.org/W1984942099","https://openalex.org/W1987458603","https://openalex.org/W1991172246","https://openalex.org/W1994917908","https://openalex.org/W1999648327","https://openalex.org/W2003250847","https://openalex.org/W2008850469","https://openalex.org/W2022015698","https://openalex.org/W2027918314","https://openalex.org/W2028572252","https://openalex.org/W2029087609","https://openalex.org/W2029120587","https://openalex.org/W2029667189","https://openalex.org/W2034144274","https://openalex.org/W2034762747","https://openalex.org/W2043255155","https://openalex.org/W2044815019","https://openalex.org/W2048233935","https://openalex.org/W2051091550","https://openalex.org/W2053015551","https://openalex.org/W2057420739","https://openalex.org/W2059392350","https://openalex.org/W2068745408","https://openalex.org/W2072732271","https://openalex.org/W2090225810","https://openalex.org/W2093446335","https://openalex.org/W2100266218","https://openalex.org/W2100736103","https://openalex.org/W2103743266","https://openalex.org/W2110142286","https://openalex.org/W2115540209","https://openalex.org/W2116275717","https://openalex.org/W2122356455","https://openalex.org/W2122536893","https://openalex.org/W2123442154","https://openalex.org/W2132592018","https://openalex.org/W2135064751","https://openalex.org/W2136094664","https://openalex.org/W2137745009","https://openalex.org/W2140555044","https://openalex.org/W2146134187","https://openalex.org/W2149026172","https://openalex.org/W2149285542","https://openalex.org/W2149285653","https://openalex.org/W2152268866","https://openalex.org/W2161151688","https://openalex.org/W2166098531","https://openalex.org/W2167785149","https://openalex.org/W2170471837","https://openalex.org/W2170711116","https://openalex.org/W2288190125","https://openalex.org/W2298851899","https://openalex.org/W2312564395","https://openalex.org/W2323405541","https://openalex.org/W2326242291","https://openalex.org/W2401285145","https://openalex.org/W2415976864","https://openalex.org/W2499356845","https://openalex.org/W2510475640","https://openalex.org/W2593563471","https://openalex.org/W2606439133","https://openalex.org/W2741372060","https://openalex.org/W2757160879","https://openalex.org/W2770064729","https://openalex.org/W2791483268","https://openalex.org/W2791904540","https://openalex.org/W2792288784","https://openalex.org/W2801664259","https://openalex.org/W2807706353","https://openalex.org/W2807883426","https://openalex.org/W2892113269","https://openalex.org/W2896064417","https://openalex.org/W2905203084","https://openalex.org/W2909036425","https://openalex.org/W2927687900","https://openalex.org/W2953018250","https://openalex.org/W2963356546","https://openalex.org/W4245176872"],"related_works":["https://openalex.org/W2128884622","https://openalex.org/W2112380088","https://openalex.org/W1715467939","https://openalex.org/W4318816969","https://openalex.org/W2161756346","https://openalex.org/W1977613337","https://openalex.org/W2075921262","https://openalex.org/W2300182960","https://openalex.org/W2338444630","https://openalex.org/W2514951647"],"abstract_inverted_index":{"The":[0,53,183,242],"optimization":[1],"approaches":[2],"classically":[3],"used":[4],"during":[5],"the":[6,16,19,39,42,60,63,73,81,128,132,145,167,197,212,223,238,245,256,267],"determination":[7],"of":[8,18,41,62,75,88,120,131,161,166,176,178,211,221,244,258,270],"protein":[9,76,240],"structure":[10],"encounter":[11],"various":[12,179],"difficulties,":[13],"especially":[14],"when":[15],"size":[17,40],"conformational":[20,82],"space":[21,44],"is":[22,91,98,141,170],"large.":[23],"Indeed,":[24],"in":[25],"such":[26],"a":[27,50,69,174,187,205],"case,":[28],"algorithmic":[29],"convergence":[30],"criteria":[31],"are":[32,113,186],"more":[33],"difficult":[34,47],"to":[35,48,158,237],"set":[36,175],"up.":[37],"Moreover,":[38],"search":[43],"makes":[45],"it":[46],"achieve":[49],"complete":[51,100],"exploration.":[52],"interval":[54,124,219],"branch-and-prune":[55,125],"(iBP)":[56],"approach,":[57],"based":[58],"on":[59,173],"reformulation":[61],"distance":[64,110],"geometry":[65,190,261],"problem":[66],"(DGP)":[67],"provides":[68],"theoretical":[70],"frame":[71],"for":[72,248],"generation":[74],"conformations,":[77],"by":[78,143,153],"systematically":[79],"sampling":[80],"space.":[83],"When":[84],"an":[85,118],"appropriate":[86],"subset":[87],"interatomic":[89],"distances":[90],"known":[92],"exactly,":[93],"this":[94,121],"worst-case":[95],"exponential-time":[96],"algorithm":[97],"provably":[99],"and":[101,152,181,204,218,262],"fixed-parameter":[102],"tractable.":[103],"These":[104],"guarantees,":[105],"however,":[106],"immediately":[107],"disappear":[108],"as":[109],"measurement":[111],"errors":[112],"introduced.":[114],"Here":[115],"we":[116],"propose":[117],"improvement":[119],"approach:":[122],"threading-augmented":[123],"(TAiBP),":[126],"where":[127],"combinatorial":[129],"explosion":[130],"original":[133],"iBP":[134],"approach":[135,169,225,247],"arising":[136],"from":[137,192,266],"its":[138],"exponential":[139],"complexity":[140],"alleviated":[142],"partitioning":[144],"input":[146],"instances":[147],"into":[148],"consecutive":[149],"peptide":[150],"fragments":[151],"using":[154],"self-organizing":[155],"maps":[156],"(SOMs)":[157],"obtain":[159],"clusters":[160],"similar":[162],"solutions.":[163],"A":[164],"validation":[165],"TAiBP":[168,224,246],"presented":[171],"here":[172],"proteins":[177,213,249],"sizes":[180],"structures.":[182],"calculation":[184],"inputs":[185],"uniform":[188],"covalent":[189,195,260],"extracted":[191],"force":[193],"field":[194],"terms,":[196],"backbone":[198],"dihedral":[199],"angles":[200],"with":[201,228,235],"error":[202],"intervals,":[203],"few":[206],"long-range":[207],"distances.":[208],"For":[209],"most":[210],"smaller":[214,231],"than":[215,232,251],"50":[216,252],"residues":[217,253],"widths":[220],"20\u00b0,":[222],"yielded":[226],"solutions":[227],"RMSD":[229],"values":[230],"3":[233],"\u00c5":[234],"respect":[236],"initial":[239],"conformation.":[241],"efficiency":[243],"larger":[250],"will":[254],"require":[255],"use":[257],"nonuniform":[259],"may":[263],"have":[264],"benefits":[265],"recent":[268],"development":[269],"residue-specific":[271],"force-fields.":[272]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
