{"id":"https://openalex.org/W2794196048","doi":"https://doi.org/10.1093/bioinformatics/bty160","title":"RapidRMSD: rapid determination of RMSDs corresponding to motions of flexible molecules","display_name":"RapidRMSD: rapid determination of RMSDs corresponding to motions of flexible molecules","publication_year":2018,"publication_date":"2018-03-15","ids":{"openalex":"https://openalex.org/W2794196048","doi":"https://doi.org/10.1093/bioinformatics/bty160","mag":"2794196048","pmid":"https://pubmed.ncbi.nlm.nih.gov/29554205"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty160","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty160","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/16/2757/25441949/bty160.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/16/2757/25441949/bty160.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036090661","display_name":"\u00c9milie Neveu","orcid":"https://orcid.org/0000-0002-2835-1502"},"institutions":[{"id":"https://openalex.org/I106785703","display_name":"Institut polytechnique de Grenoble","ror":"https://ror.org/05sbt2524","country_code":"FR","type":"education","lineage":["https://openalex.org/I106785703","https://openalex.org/I899635006"]},{"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/I4210101348","display_name":"Centre Inria de l'Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/00n8d6z93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]},{"id":"https://openalex.org/I4210149092","display_name":"Laboratoire Jean Kuntzmann","ror":"https://ror.org/04ett5b41","country_code":"FR","type":"facility","lineage":["https://openalex.org/I106785703","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I4210149092","https://openalex.org/I899635006","https://openalex.org/I899635006"]},{"id":"https://openalex.org/I899635006","display_name":"Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/02rx3b187","country_code":"FR","type":"education","lineage":["https://openalex.org/I899635006"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH","FR"],"is_corresponding":false,"raw_author_name":"Emilie Neveu","raw_affiliation_strings":["Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland","Inria/Univ. Grenoble Alpes/LJK-CNRS, Grenoble, France","NANO-D - Algorithms for Modeling and Simulation of Nanosystems (Inria GIANT DRT/LETI/DACLE Batiment 51C - Minatec Campus 17 rue des Martyrs 38054 Grenoble Cedex - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I97565354"]},{"raw_affiliation_string":"Inria/Univ. Grenoble Alpes/LJK-CNRS, Grenoble, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210101348","https://openalex.org/I4210149092","https://openalex.org/I899635006"]},{"raw_affiliation_string":"NANO-D - Algorithms for Modeling and Simulation of Nanosystems (Inria GIANT DRT/LETI/DACLE Batiment 51C - Minatec Campus 17 rue des Martyrs 38054 Grenoble Cedex - France)","institution_ids":["https://openalex.org/I106785703","https://openalex.org/I4210101348"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085541533","display_name":"Petr Popov","orcid":"https://orcid.org/0000-0003-3745-7154"},"institutions":[{"id":"https://openalex.org/I106785703","display_name":"Institut polytechnique de Grenoble","ror":"https://ror.org/05sbt2524","country_code":"FR","type":"education","lineage":["https://openalex.org/I106785703","https://openalex.org/I899635006"]},{"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/I153845743","display_name":"Moscow Institute of Physics and Technology","ror":"https://ror.org/00v0z9322","country_code":"RU","type":"education","lineage":["https://openalex.org/I153845743"]},{"id":"https://openalex.org/I4210101348","display_name":"Centre Inria de l'Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/00n8d6z93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]},{"id":"https://openalex.org/I4210149092","display_name":"Laboratoire Jean Kuntzmann","ror":"https://ror.org/04ett5b41","country_code":"FR","type":"facility","lineage":["https://openalex.org/I106785703","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I4210149092","https://openalex.org/I899635006","https://openalex.org/I899635006"]},{"id":"https://openalex.org/I899635006","display_name":"Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/02rx3b187","country_code":"FR","type":"education","lineage":["https://openalex.org/I899635006"]}],"countries":["FR","RU"],"is_corresponding":false,"raw_author_name":"Petr Popov","raw_affiliation_strings":["Inria/Univ. Grenoble Alpes/LJK-CNRS, Grenoble, France","Moscow Institute of Physics and Technology, Dolgoprudniy, Russia","MIPT - Moscow Institute of Physics and Technology [Moscow] (9 Institutskiy per., Dolgoprudny, Moscow Region, 141701 - Russia)","NANO-D - Algorithms for Modeling and Simulation of Nanosystems (Inria GIANT DRT/LETI/DACLE Batiment 51C - Minatec Campus 17 rue des Martyrs 38054 Grenoble Cedex - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inria/Univ. Grenoble Alpes/LJK-CNRS, Grenoble, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210101348","https://openalex.org/I4210149092","https://openalex.org/I899635006"]},{"raw_affiliation_string":"Moscow Institute of Physics and Technology, Dolgoprudniy, Russia","institution_ids":["https://openalex.org/I153845743"]},{"raw_affiliation_string":"MIPT - Moscow Institute of Physics and Technology [Moscow] (9 Institutskiy per., Dolgoprudny, Moscow Region, 141701 - Russia)","institution_ids":["https://openalex.org/I153845743"]},{"raw_affiliation_string":"NANO-D - Algorithms for Modeling and Simulation of Nanosystems (Inria GIANT DRT/LETI/DACLE Batiment 51C - Minatec Campus 17 rue des Martyrs 38054 Grenoble Cedex - France)","institution_ids":["https://openalex.org/I106785703","https://openalex.org/I4210101348"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048946821","display_name":"Alexandre Hoffmann","orcid":"https://orcid.org/0000-0002-0948-8132"},"institutions":[{"id":"https://openalex.org/I106785703","display_name":"Institut polytechnique de Grenoble","ror":"https://ror.org/05sbt2524","country_code":"FR","type":"education","lineage":["https://openalex.org/I106785703","https://openalex.org/I899635006"]},{"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/I4210101348","display_name":"Centre Inria de l'Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/00n8d6z93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]},{"id":"https://openalex.org/I4210149092","display_name":"Laboratoire Jean Kuntzmann","ror":"https://ror.org/04ett5b41","country_code":"FR","type":"facility","lineage":["https://openalex.org/I106785703","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I4210149092","https://openalex.org/I899635006","https://openalex.org/I899635006"]},{"id":"https://openalex.org/I899635006","display_name":"Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/02rx3b187","country_code":"FR","type":"education","lineage":["https://openalex.org/I899635006"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Alexandre Hoffmann","raw_affiliation_strings":["Inria/Univ. Grenoble Alpes/LJK-CNRS, Grenoble, France","NANO-D - Algorithms for Modeling and Simulation of Nanosystems (Inria GIANT DRT/LETI/DACLE Batiment 51C - Minatec Campus 17 rue des Martyrs 38054 Grenoble Cedex - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inria/Univ. Grenoble Alpes/LJK-CNRS, Grenoble, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210101348","https://openalex.org/I4210149092","https://openalex.org/I899635006"]},{"raw_affiliation_string":"NANO-D - Algorithms for Modeling and Simulation of Nanosystems (Inria GIANT DRT/LETI/DACLE Batiment 51C - Minatec Campus 17 rue des Martyrs 38054 Grenoble Cedex - France)","institution_ids":["https://openalex.org/I106785703","https://openalex.org/I4210101348"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061170647","display_name":"Angelo Migliosi","orcid":null},"institutions":[{"id":"https://openalex.org/I186903577","display_name":"University of Luxembourg","ror":"https://ror.org/036x5ad56","country_code":"LU","type":"education","lineage":["https://openalex.org/I186903577"]},{"id":"https://openalex.org/I4210134190","display_name":"Recherches Scientifiques Luxembourg","ror":"https://ror.org/0333e3w09","country_code":"LU","type":"facility","lineage":["https://openalex.org/I4210134190"]}],"countries":["LU"],"is_corresponding":false,"raw_author_name":"Angelo Migliosi","raw_affiliation_strings":["Facult\u00e9 des Sciences, de la Technologie et de la Communication, University of Luxembourg, Luxembourg, Luxembourg","CSC - Computer Science and Communications Research Unit [Luxembourg] (Campus Kirchberg 6, rue Richard Coudenhove-Kalergi L-1359 Luxembourg LUXEMBOURG - Luxembourg)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Facult\u00e9 des Sciences, de la Technologie et de la Communication, University of Luxembourg, Luxembourg, Luxembourg","institution_ids":["https://openalex.org/I186903577"]},{"raw_affiliation_string":"CSC - Computer Science and Communications Research Unit [Luxembourg] (Campus Kirchberg 6, rue Richard Coudenhove-Kalergi L-1359 Luxembourg LUXEMBOURG - Luxembourg)","institution_ids":["https://openalex.org/I4210134190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050229692","display_name":"Xavier Besseron","orcid":"https://orcid.org/0000-0002-7783-2185"},"institutions":[{"id":"https://openalex.org/I186903577","display_name":"University of Luxembourg","ror":"https://ror.org/036x5ad56","country_code":"LU","type":"education","lineage":["https://openalex.org/I186903577"]},{"id":"https://openalex.org/I4210134190","display_name":"Recherches Scientifiques Luxembourg","ror":"https://ror.org/0333e3w09","country_code":"LU","type":"facility","lineage":["https://openalex.org/I4210134190"]}],"countries":["LU"],"is_corresponding":false,"raw_author_name":"Xavier Besseron","raw_affiliation_strings":["Facult\u00e9 des Sciences, de la Technologie et de la Communication, University of Luxembourg, Luxembourg, Luxembourg","CSC - Computer Science and Communications Research Unit [Luxembourg] (Campus Kirchberg 6, rue Richard Coudenhove-Kalergi L-1359 Luxembourg LUXEMBOURG - Luxembourg)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Facult\u00e9 des Sciences, de la Technologie et de la Communication, University of Luxembourg, Luxembourg, Luxembourg","institution_ids":["https://openalex.org/I186903577"]},{"raw_affiliation_string":"CSC - Computer Science and Communications Research Unit [Luxembourg] (Campus Kirchberg 6, rue Richard Coudenhove-Kalergi L-1359 Luxembourg LUXEMBOURG - Luxembourg)","institution_ids":["https://openalex.org/I4210134190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107678280","display_name":"Gr\u00e9goire Danoy","orcid":"https://orcid.org/0000-0001-9419-4210"},"institutions":[{"id":"https://openalex.org/I186903577","display_name":"University of Luxembourg","ror":"https://ror.org/036x5ad56","country_code":"LU","type":"education","lineage":["https://openalex.org/I186903577"]},{"id":"https://openalex.org/I4210134190","display_name":"Recherches Scientifiques Luxembourg","ror":"https://ror.org/0333e3w09","country_code":"LU","type":"facility","lineage":["https://openalex.org/I4210134190"]}],"countries":["LU"],"is_corresponding":false,"raw_author_name":"Gr\u00e9goire Danoy","raw_affiliation_strings":["Facult\u00e9 des Sciences, de la Technologie et de la Communication, University of Luxembourg, Luxembourg, Luxembourg","CSC - Computer Science and Communications Research Unit [Luxembourg] (Campus Kirchberg 6, rue Richard Coudenhove-Kalergi L-1359 Luxembourg LUXEMBOURG - Luxembourg)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Facult\u00e9 des Sciences, de la Technologie et de la Communication, University of Luxembourg, Luxembourg, Luxembourg","institution_ids":["https://openalex.org/I186903577"]},{"raw_affiliation_string":"CSC - Computer Science and Communications Research Unit [Luxembourg] (Campus Kirchberg 6, rue Richard Coudenhove-Kalergi L-1359 Luxembourg LUXEMBOURG - Luxembourg)","institution_ids":["https://openalex.org/I4210134190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058311932","display_name":"Pascal Bouvry","orcid":"https://orcid.org/0000-0001-9338-2834"},"institutions":[{"id":"https://openalex.org/I186903577","display_name":"University of Luxembourg","ror":"https://ror.org/036x5ad56","country_code":"LU","type":"education","lineage":["https://openalex.org/I186903577"]},{"id":"https://openalex.org/I4210134190","display_name":"Recherches Scientifiques Luxembourg","ror":"https://ror.org/0333e3w09","country_code":"LU","type":"facility","lineage":["https://openalex.org/I4210134190"]}],"countries":["LU"],"is_corresponding":false,"raw_author_name":"Pascal Bouvry","raw_affiliation_strings":["Facult\u00e9 des Sciences, de la Technologie et de la Communication, University of Luxembourg, Luxembourg, Luxembourg","CSC - Computer Science and Communications Research Unit [Luxembourg] (Campus Kirchberg 6, rue Richard Coudenhove-Kalergi L-1359 Luxembourg LUXEMBOURG - Luxembourg)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Facult\u00e9 des Sciences, de la Technologie et de la Communication, University of Luxembourg, Luxembourg, Luxembourg","institution_ids":["https://openalex.org/I186903577"]},{"raw_affiliation_string":"CSC - Computer Science and Communications Research Unit [Luxembourg] (Campus Kirchberg 6, rue Richard Coudenhove-Kalergi L-1359 Luxembourg LUXEMBOURG - Luxembourg)","institution_ids":["https://openalex.org/I4210134190"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009307435","display_name":"Sergei Grudinin","orcid":"https://orcid.org/0000-0002-1903-7220"},"institutions":[{"id":"https://openalex.org/I106785703","display_name":"Institut polytechnique de Grenoble","ror":"https://ror.org/05sbt2524","country_code":"FR","type":"education","lineage":["https://openalex.org/I106785703","https://openalex.org/I899635006"]},{"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/I4210101348","display_name":"Centre Inria de l'Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/00n8d6z93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]},{"id":"https://openalex.org/I4210149092","display_name":"Laboratoire Jean Kuntzmann","ror":"https://ror.org/04ett5b41","country_code":"FR","type":"facility","lineage":["https://openalex.org/I106785703","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I4210149092","https://openalex.org/I899635006","https://openalex.org/I899635006"]},{"id":"https://openalex.org/I899635006","display_name":"Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/02rx3b187","country_code":"FR","type":"education","lineage":["https://openalex.org/I899635006"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Sergei Grudinin","raw_affiliation_strings":["Inria/Univ. Grenoble Alpes/LJK-CNRS, Grenoble, France","NANO-D - Algorithms for Modeling and Simulation of Nanosystems (Inria GIANT DRT/LETI/DACLE Batiment 51C - Minatec Campus 17 rue des Martyrs 38054 Grenoble Cedex - France)"],"raw_orcid":"https://orcid.org/0000-0002-1903-7220","affiliations":[{"raw_affiliation_string":"Inria/Univ. Grenoble Alpes/LJK-CNRS, Grenoble, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210101348","https://openalex.org/I4210149092","https://openalex.org/I899635006"]},{"raw_affiliation_string":"NANO-D - Algorithms for Modeling and Simulation of Nanosystems (Inria GIANT DRT/LETI/DACLE Batiment 51C - Minatec Campus 17 rue des Martyrs 38054 Grenoble Cedex - France)","institution_ids":["https://openalex.org/I106785703","https://openalex.org/I4210101348"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5009307435"],"corresponding_institution_ids":["https://openalex.org/I106785703","https://openalex.org/I1294671590","https://openalex.org/I4210101348","https://openalex.org/I4210149092","https://openalex.org/I899635006"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9898,"has_fulltext":true,"cited_by_count":35,"citation_normalized_percentile":{"value":0.74195477,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"34","issue":"16","first_page":"2757","last_page":"2765"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.4212000072002411,"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":0.4212000072002411,"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/T11686","display_name":"Dendrimers and Hyperbranched Polymers","score":0.07240000367164612,"subfield":{"id":"https://openalex.org/subfields/2507","display_name":"Polymers and Plastics"},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.04780000075697899,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5914690494537354},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.40219539403915405},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.3618631958961487},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33528900146484375},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.24230194091796875}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5914690494537354},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.40219539403915405},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3618631958961487},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33528900146484375},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.24230194091796875}],"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":"D009038","descriptor_name":"Motion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009038","descriptor_name":"Motion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009038","descriptor_name":"Motion","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018583","descriptor_name":"Pliability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018583","descriptor_name":"Pliability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018583","descriptor_name":"Pliability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","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":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component 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":6,"locations":[{"id":"doi:10.1093/bioinformatics/bty160","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty160","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/16/2757/25441949/bty160.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29554205","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29554205","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:HAL:hal-01735214v1","is_oa":true,"landing_page_url":"https://inria.hal.science/hal-01735214","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":"Bioinformatics, 2018, 34 (16), pp.2757-2765. &#x27E8;10.1093/bioinformatics/bty160&#x27E9;","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:iris.unil.ch:iris/114119","is_oa":false,"landing_page_url":"https://iris.unil.ch/handle/iris/114119","pdf_url":null,"source":{"id":"https://openalex.org/S7407055444","display_name":"IRIS","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"review article"},{"id":"pmh:oai:orbilu.uni.lu:10993/35253","is_oa":false,"landing_page_url":"https://orbilu.uni.lu/handle/10993/35253","pdf_url":null,"source":{"id":"https://openalex.org/S4306401815","display_name":"Open Repository and Bibliography (University of Luxembourg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I186903577","host_organization_name":"University of Luxembourg","host_organization_lineage":["https://openalex.org/I186903577"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics (2018)","raw_type":"http://purl.org/coar/resource_type/c_6501"},{"id":"pmh:oai:serval.unil.ch:BIB_61A160F529BC","is_oa":false,"landing_page_url":"https://serval.unil.ch/notice/serval:BIB_61A160F529BC","pdf_url":null,"source":{"id":"https://openalex.org/S4306401797","display_name":"SERVAL (Universit\u00e9 de Lausanne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210093590","host_organization_name":"Swiss School of Archaeology in Greece","host_organization_lineage":["https://openalex.org/I4210093590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, vol. 34, no. 16, pp. 2757-2765","raw_type":"info:eu-repo/semantics/review"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty160","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty160","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/16/2757/25441949/bty160.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1765763729","display_name":null,"funder_award_id":"ANR-11-MONU-006-01","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G2914748784","display_name":"Polynomial Expansions of Protein Structures and Interactions","funder_award_id":"ANR-11-MONU-0006","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G3356476482","display_name":null,"funder_award_id":"16-14-10273","funder_id":"https://openalex.org/F4320324099","funder_display_name":"Russian Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320324099","display_name":"Russian Science Foundation","ror":"https://ror.org/03y2gwe85"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2794196048.pdf","grobid_xml":"https://content.openalex.org/works/W2794196048.grobid-xml"},"referenced_works_count":58,"referenced_works":["https://openalex.org/W1030883578","https://openalex.org/W1658199422","https://openalex.org/W1834365857","https://openalex.org/W1843396089","https://openalex.org/W1968407616","https://openalex.org/W1969404979","https://openalex.org/W1969875513","https://openalex.org/W1975642089","https://openalex.org/W1979284950","https://openalex.org/W1984940101","https://openalex.org/W1993267444","https://openalex.org/W1993951624","https://openalex.org/W2005303195","https://openalex.org/W2009129583","https://openalex.org/W2009696322","https://openalex.org/W2010956452","https://openalex.org/W2011616792","https://openalex.org/W2012042639","https://openalex.org/W2016586584","https://openalex.org/W2022058405","https://openalex.org/W2023857477","https://openalex.org/W2027486315","https://openalex.org/W2036000659","https://openalex.org/W2046187342","https://openalex.org/W2048643046","https://openalex.org/W2052963427","https://openalex.org/W2069777230","https://openalex.org/W2087151779","https://openalex.org/W2088906583","https://openalex.org/W2090183113","https://openalex.org/W2097031841","https://openalex.org/W2097642323","https://openalex.org/W2099286799","https://openalex.org/W2101017457","https://openalex.org/W2102449622","https://openalex.org/W2108852701","https://openalex.org/W2113554569","https://openalex.org/W2115451817","https://openalex.org/W2122576346","https://openalex.org/W2125696348","https://openalex.org/W2126105956","https://openalex.org/W2127868702","https://openalex.org/W2128175348","https://openalex.org/W2133712572","https://openalex.org/W2135983089","https://openalex.org/W2137321308","https://openalex.org/W2138871907","https://openalex.org/W2143047148","https://openalex.org/W2150472159","https://openalex.org/W2153413946","https://openalex.org/W2153983456","https://openalex.org/W2158528359","https://openalex.org/W2160223767","https://openalex.org/W2169085737","https://openalex.org/W2320535368","https://openalex.org/W2541404351","https://openalex.org/W2604474471","https://openalex.org/W2789020169"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W4391913857"],"abstract_inverted_index":{"Motivation:":[0],"The":[1,122,247],"root":[2],"mean":[3],"square":[4],"deviation":[5],"(RMSD)":[6],"is":[7,127,164,243,257],"one":[8],"of":[9,22,34,51,57,77,88,98,109,124,132,139,151,181,190,254],"the":[10,23,32,44,65,70,74,86,89,99,103,130,136,149,159,169,179,205,227,233,239],"most":[11],"used":[12],"similarity":[13],"criteria":[14],"in":[15,36,129,220,230],"structural":[16,212,249],"biology":[17],"and":[18,134,194,215,223,252],"bioinformatics.":[19],"Standard":[20],"computation":[21,172],"RMSD":[24,40,71,140,171],"has":[25],"a":[26,37,78,106],"linear":[27,128],"complexity":[28],"with":[29,105,113],"respect":[30],"to":[31,68,73,157,168,203,208,217],"number":[33,131,150],"atoms":[35,133],"molecule,":[38],"making":[39],"calculations":[41],"time-consuming":[42],"for":[43,173],"large-scale":[45,174],"modeling":[46,175],"applications,":[47],"such":[48],"as":[49,232],"assessment":[50],"molecular":[52,60,144,195,213],"docking":[53,192],"predictions":[54],"or":[55,117],"clustering":[56,186,189,253],"spatially":[58],"proximate":[59],"conformations.":[61],"Previously,":[62],"we":[63,83],"introduced":[64],"RigidRMSD":[66],"algorithm":[67,126,163,228],"compute":[69],"corresponding":[72],"rigid-body":[75,90],"motion":[76],"molecule.":[79,100],"In":[80],"this":[81],"study,":[82],"go":[84],"beyond":[85],"limits":[87],"approximation":[91],"by":[92,238],"taking":[93],"into":[94],"account":[95],"conformational":[96],"flexibility":[97,104],"We":[101,177,199,225],"model":[102,158],"reduced":[107],"set":[108],"collective":[110,152],"motions":[111,153],"computed":[112],"e.g.":[114],"normal":[115],"modes":[116],"principal":[118],"component":[119],"analysis.":[120],"Results:":[121],"initialization":[123],"our":[125,162,182],"all":[135],"subsequent":[137],"evaluations":[138],"values":[141],"between":[142],"flexible":[143,191],"conformations":[145],"depend":[146],"only":[147],"on":[148,184],"that":[154],"are":[155,265],"selected":[156],"flexibility.":[160],"Therefore,":[161],"much":[165],"faster":[166],"compared":[167],"standard":[170],"applications.":[176],"demonstrate":[178,201],"efficiency":[180],"method":[183],"several":[185],"examples,":[187],"including":[188],"results":[193],"dynamics":[196],"(MD)":[197],"trajectories.":[198],"also":[200],"how":[202,216],"use":[204,218],"presented":[206],"formalism":[207],"generate":[209],"pseudo-random":[210],"constant-RMSD":[211,248],"ensembles":[214],"these":[219],"cross-docking.":[221],"Availability":[222],"implementation:":[224],"provide":[226],"written":[229],"C++":[231],"open-source":[234],"RapidRMSD":[235],"library":[236],"governed":[237],"BSD-compatible":[240],"license,":[241],"which":[242],"available":[244,258,266],"at":[245,259,267],"http://team.inria.fr/nano-d/software/RapidRMSD/.":[246],"ensemble":[250],"application":[251],"MD":[255],"trajectories":[256],"http://team.inria.fr/nano-d/software/nolb-normal-modes/.":[260],"Supplementary":[261,263],"information:":[262],"data":[264],"Bioinformatics":[268],"online.":[269]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":3}],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2025-10-10T00:00:00"}
