{"id":"https://openalex.org/W2596256463","doi":"https://doi.org/10.1021/acs.jcim.6b00646","title":"Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins","display_name":"Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins","publication_year":2017,"publication_date":"2017-03-16","ids":{"openalex":"https://openalex.org/W2596256463","doi":"https://doi.org/10.1021/acs.jcim.6b00646","mag":"2596256463","pmid":"https://pubmed.ncbi.nlm.nih.gov/28301154"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.6b00646","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00646","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":"http://americanae.aecid.es/americanae/es/registros/registro.do?tipoRegistro=MTD&idBib=3911297","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048938166","display_name":"Rodrigo Cossio-P\u00e9rez","orcid":"https://orcid.org/0000-0002-4407-7179"},"institutions":[{"id":"https://openalex.org/I138504249","display_name":"National University of Quilmes","ror":"https://ror.org/01r53hz59","country_code":"AR","type":"education","lineage":["https://openalex.org/I138504249"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"Rodrigo Cossio-P\u00e9rez","raw_affiliation_strings":["Departamento de Ciencia y\rTecnolog\u00eda, Universidad Nacional de Quilmes, S\u00e1enz\rPe\u00f1a 352, B1876BXD Bernal, Argentina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Ciencia y\rTecnolog\u00eda, Universidad Nacional de Quilmes, S\u00e1enz\rPe\u00f1a 352, B1876BXD Bernal, Argentina","institution_ids":["https://openalex.org/I138504249"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033947352","display_name":"Juliana Palma","orcid":"https://orcid.org/0000-0002-0761-0253"},"institutions":[{"id":"https://openalex.org/I138504249","display_name":"National University of Quilmes","ror":"https://ror.org/01r53hz59","country_code":"AR","type":"education","lineage":["https://openalex.org/I138504249"]}],"countries":["AR"],"is_corresponding":true,"raw_author_name":"Juliana Palma","raw_affiliation_strings":["Departamento de Ciencia y\rTecnolog\u00eda, Universidad Nacional de Quilmes, S\u00e1enz\rPe\u00f1a 352, B1876BXD Bernal, Argentina"],"raw_orcid":"https://orcid.org/0000-0002-0761-0253","affiliations":[{"raw_affiliation_string":"Departamento de Ciencia y\rTecnolog\u00eda, Universidad Nacional de Quilmes, S\u00e1enz\rPe\u00f1a 352, B1876BXD Bernal, Argentina","institution_ids":["https://openalex.org/I138504249"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052097735","display_name":"Gustavo Pierdominici\u2010Sottile","orcid":"https://orcid.org/0000-0003-3792-4509"},"institutions":[{"id":"https://openalex.org/I138504249","display_name":"National University of Quilmes","ror":"https://ror.org/01r53hz59","country_code":"AR","type":"education","lineage":["https://openalex.org/I138504249"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"Gustavo Pierdominici-Sottile","raw_affiliation_strings":["Departamento de Ciencia y\rTecnolog\u00eda, Universidad Nacional de Quilmes, S\u00e1enz\rPe\u00f1a 352, B1876BXD Bernal, Argentina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Ciencia y\rTecnolog\u00eda, Universidad Nacional de Quilmes, S\u00e1enz\rPe\u00f1a 352, B1876BXD Bernal, Argentina","institution_ids":["https://openalex.org/I138504249"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5033947352"],"corresponding_institution_ids":["https://openalex.org/I138504249"],"apc_list":null,"apc_paid":null,"fwci":0.6084,"has_fulltext":false,"cited_by_count":39,"citation_normalized_percentile":{"value":0.64926283,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"57","issue":"4","first_page":"826","last_page":"834"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998000264167786,"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":0.9998000264167786,"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/T11177","display_name":"Spectroscopy and Quantum Chemical Studies","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11809","display_name":"Advanced NMR Techniques and Applications","score":0.994700014591217,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/principal-component-analysis","display_name":"Principal component analysis","score":0.7982635498046875},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.6754368543624878},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.665855884552002},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.6507247686386108},{"id":"https://openalex.org/keywords/component","display_name":"Component (thermodynamics)","score":0.6458167433738708},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.5280550122261047},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5190723538398743},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.4496517479419708},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3836180865764618},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.30088159441947937},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.26977306604385376},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.21197780966758728},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15380528569221497},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.13743159174919128}],"concepts":[{"id":"https://openalex.org/C27438332","wikidata":"https://www.wikidata.org/wiki/Q2873","display_name":"Principal component analysis","level":2,"score":0.7982635498046875},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6754368543624878},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.665855884552002},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.6507247686386108},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.6458167433738708},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.5280550122261047},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5190723538398743},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.4496517479419708},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3836180865764618},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.30088159441947937},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.26977306604385376},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.21197780966758728},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15380528569221497},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.13743159174919128},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D009113","descriptor_name":"Muramidase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009113","descriptor_name":"Muramidase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009113","descriptor_name":"Muramidase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009113","descriptor_name":"Muramidase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009113","descriptor_name":"Muramidase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009113","descriptor_name":"Muramidase","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","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":4,"locations":[{"id":"doi:10.1021/acs.jcim.6b00646","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00646","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:28301154","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28301154","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:americanae.aecid.es:3911297","is_oa":true,"landing_page_url":"http://americanae.aecid.es/americanae/es/registros/registro.do?tipoRegistro=MTD&idBib=3911297","pdf_url":null,"source":{"id":"https://openalex.org/S4306400786","display_name":"Americanae (AECID Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"reponame:CONICET Digital (CONICET)","raw_type":"http://purl.org/coar/resource_type/c_6501"},{"id":"pmh:oai:ri.conicet.gov.ar:11336/72866","is_oa":true,"landing_page_url":"http://hdl.handle.net/11336/72866","pdf_url":null,"source":{"id":"https://openalex.org/S4306402641","display_name":"LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Cient\u00edficas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4383465926","host_organization_name":"LA Referencia","host_organization_lineage":["https://openalex.org/I4383465926"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"reponame:CONICET Digital (CONICET)","raw_type":"http://purl.org/coar/resource_type/c_6501"}],"best_oa_location":{"id":"pmh:oai:americanae.aecid.es:3911297","is_oa":true,"landing_page_url":"http://americanae.aecid.es/americanae/es/registros/registro.do?tipoRegistro=MTD&idBib=3911297","pdf_url":null,"source":{"id":"https://openalex.org/S4306400786","display_name":"Americanae (AECID Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"reponame:CONICET Digital (CONICET)","raw_type":"http://purl.org/coar/resource_type/c_6501"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2243952939","display_name":null,"funder_award_id":"1402/15","funder_id":"https://openalex.org/F4320325873","funder_display_name":"Universidad Nacional de Quilmes"},{"id":"https://openalex.org/G2815644054","display_name":"Estudios experimentales y te\u00f3ricos sobre los mecanismos moleculares del funcionamiento de canales y transportadores trans-membrana","funder_award_id":"11220130100260CO","funder_id":"https://openalex.org/F4320321594","funder_display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas"}],"funders":[{"id":"https://openalex.org/F4320321594","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59"},{"id":"https://openalex.org/F4320325873","display_name":"Universidad Nacional de Quilmes","ror":"https://ror.org/01r53hz59"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":56,"referenced_works":["https://openalex.org/W94305608","https://openalex.org/W1518373477","https://openalex.org/W1569273074","https://openalex.org/W1584026477","https://openalex.org/W1933268512","https://openalex.org/W1935237622","https://openalex.org/W1966111577","https://openalex.org/W1967618914","https://openalex.org/W1972110728","https://openalex.org/W1975734016","https://openalex.org/W1976248692","https://openalex.org/W1976993208","https://openalex.org/W1977867181","https://openalex.org/W1985716674","https://openalex.org/W1990387274","https://openalex.org/W1990996314","https://openalex.org/W1995524958","https://openalex.org/W1997701017","https://openalex.org/W1998412941","https://openalex.org/W1998875094","https://openalex.org/W2015110061","https://openalex.org/W2016267980","https://openalex.org/W2016280956","https://openalex.org/W2017318572","https://openalex.org/W2024225780","https://openalex.org/W2031092627","https://openalex.org/W2033350048","https://openalex.org/W2037760012","https://openalex.org/W2040503203","https://openalex.org/W2041051514","https://openalex.org/W2047842317","https://openalex.org/W2054156098","https://openalex.org/W2057197276","https://openalex.org/W2061059141","https://openalex.org/W2063328932","https://openalex.org/W2064825879","https://openalex.org/W2071656198","https://openalex.org/W2074160718","https://openalex.org/W2075460992","https://openalex.org/W2080752658","https://openalex.org/W2081231020","https://openalex.org/W2083000982","https://openalex.org/W2093965573","https://openalex.org/W2099793312","https://openalex.org/W2109102515","https://openalex.org/W2121220560","https://openalex.org/W2123182960","https://openalex.org/W2132589721","https://openalex.org/W2141519313","https://openalex.org/W2141839673","https://openalex.org/W2150092099","https://openalex.org/W2156350373","https://openalex.org/W2169138936","https://openalex.org/W2345406112","https://openalex.org/W2511010414","https://openalex.org/W3105364218"],"related_works":["https://openalex.org/W1975632186","https://openalex.org/W3027745756","https://openalex.org/W3205213561","https://openalex.org/W2531880140","https://openalex.org/W2126145365","https://openalex.org/W2036609560","https://openalex.org/W346861917","https://openalex.org/W3024018414","https://openalex.org/W1542592062","https://openalex.org/W1773535258"],"abstract_inverted_index":{"Principal":[0],"component":[1],"analysis":[2],"is":[3],"a":[4,30],"technique":[5,28],"widely":[6],"used":[7],"for":[8],"studying":[9],"the":[10,27,38,52,55,60,63,66,69,81],"movements":[11],"of":[12,23,62,68],"proteins":[13],"using":[14],"data":[15],"collected":[16],"from":[17,54],"molecular":[18],"dynamics":[19],"simulations.":[20],"In":[21,41],"spite":[22],"its":[24],"extensive":[25],"use,":[26],"has":[29],"serious":[31],"drawback:":[32],"equivalent":[33,48],"simulations":[34],"do":[35],"not":[36],"afford":[37],"same":[39],"PC-modes.":[40],"this":[42],"article,":[43],"we":[44],"show":[45],"that":[46],"concatenating":[47],"trajectories":[49,79],"and":[50],"calculating":[51],"PC-modes":[53],"concatenated":[56,82],"one":[57],"significantly":[58],"enhances":[59],"reproducibility":[61],"results.":[64],"Moreover,":[65],"consistency":[67],"modes":[70],"can":[71],"be":[72],"systematically":[73],"improved":[74],"by":[75],"adding":[76],"more":[77],"individual":[78],"to":[80],"one.":[83]},"counts_by_year":[{"year":2026,"cited_by_count":9},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}