{"id":"https://openalex.org/W2107278499","doi":"https://doi.org/10.1093/bioinformatics/btu822","title":"Epock: rapid analysis of protein pocket dynamics","display_name":"Epock: rapid analysis of protein pocket dynamics","publication_year":2014,"publication_date":"2014-12-12","ids":{"openalex":"https://openalex.org/W2107278499","doi":"https://doi.org/10.1093/bioinformatics/btu822","mag":"2107278499","pmid":"https://pubmed.ncbi.nlm.nih.gov/25505095"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu822","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu822","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/9/1478/17085621/btu822.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/9/1478/17085621/btu822.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020115791","display_name":"Benoist Laurent","orcid":null},"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/I169173203","display_name":"D\u00e9l\u00e9gation Paris 7","ror":"https://ror.org/00bw5n526","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488","https://openalex.org/I169173203"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210091437","display_name":"Sorbonne Paris Cit\u00e9","ror":"https://ror.org/001z21q04","country_code":"FR","type":"other","lineage":["https://openalex.org/I4210091437"]},{"id":"https://openalex.org/I4210094297","display_name":"Laboratoire de Biochimie Th\u00e9orique","ror":"https://ror.org/00nvjgv40","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4210094297","https://openalex.org/I4210128300"]}],"countries":["FR","GB"],"is_corresponding":true,"raw_author_name":"Benoist Laurent","raw_affiliation_strings":["1 Laboratoire de Biochimie Th\u00e9orique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cit\u00e9, F-75005 Paris, France and 2Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK","LBT (UPR_9080) - Laboratoire de biochimie th\u00e9orique [Paris] (13 Rue Pierre et Marie Curie 75005 PARIS - France)","Universite\u0301 Paris Diderot, Sorbonne Paris Cite\u0301, Paris, France (France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Laboratoire de Biochimie Th\u00e9orique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cit\u00e9, F-75005 Paris, France and 2Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I169173203","https://openalex.org/I204730241","https://openalex.org/I40120149","https://openalex.org/I4210091437","https://openalex.org/I4210094297"]},{"raw_affiliation_string":"LBT (UPR_9080) - Laboratoire de biochimie th\u00e9orique [Paris] (13 Rue Pierre et Marie Curie 75005 PARIS - France)","institution_ids":["https://openalex.org/I4210094297"]},{"raw_affiliation_string":"Universite\u0301 Paris Diderot, Sorbonne Paris Cite\u0301, Paris, France (France)","institution_ids":["https://openalex.org/I169173203","https://openalex.org/I204730241","https://openalex.org/I4210091437"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082706216","display_name":"Matthieu Chavent","orcid":"https://orcid.org/0000-0003-4524-4773"},"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/I169173203","display_name":"D\u00e9l\u00e9gation Paris 7","ror":"https://ror.org/00bw5n526","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488","https://openalex.org/I169173203"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210091437","display_name":"Sorbonne Paris Cit\u00e9","ror":"https://ror.org/001z21q04","country_code":"FR","type":"other","lineage":["https://openalex.org/I4210091437"]},{"id":"https://openalex.org/I4210094297","display_name":"Laboratoire de Biochimie Th\u00e9orique","ror":"https://ror.org/00nvjgv40","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4210094297","https://openalex.org/I4210128300"]}],"countries":["FR","GB"],"is_corresponding":false,"raw_author_name":"Matthieu Chavent","raw_affiliation_strings":["1 Laboratoire de Biochimie Th\u00e9orique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cit\u00e9, F-75005 Paris, France and 2Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK","SBCB - Structural Bioinformatics and Computational Biochemistry [Oxford] (University of Oxford\r\nSouth Parks Road\r\nOxford OX1 3QU - United Kingdom)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Laboratoire de Biochimie Th\u00e9orique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cit\u00e9, F-75005 Paris, France and 2Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I169173203","https://openalex.org/I204730241","https://openalex.org/I40120149","https://openalex.org/I4210091437","https://openalex.org/I4210094297"]},{"raw_affiliation_string":"SBCB - Structural Bioinformatics and Computational Biochemistry [Oxford] (University of Oxford\r\nSouth Parks Road\r\nOxford OX1 3QU - United Kingdom)","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059832457","display_name":"Tristan Cragnolini","orcid":"https://orcid.org/0000-0001-6917-7056"},"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/I169173203","display_name":"D\u00e9l\u00e9gation Paris 7","ror":"https://ror.org/00bw5n526","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488","https://openalex.org/I169173203"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210091437","display_name":"Sorbonne Paris Cit\u00e9","ror":"https://ror.org/001z21q04","country_code":"FR","type":"other","lineage":["https://openalex.org/I4210091437"]},{"id":"https://openalex.org/I4210094297","display_name":"Laboratoire de Biochimie Th\u00e9orique","ror":"https://ror.org/00nvjgv40","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4210094297","https://openalex.org/I4210128300"]}],"countries":["FR","GB"],"is_corresponding":false,"raw_author_name":"Tristan Cragnolini","raw_affiliation_strings":["1 Laboratoire de Biochimie Th\u00e9orique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cit\u00e9, F-75005 Paris, France and 2Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK","LBT (UPR_9080) - Laboratoire de biochimie th\u00e9orique [Paris] (13 Rue Pierre et Marie Curie 75005 PARIS - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Laboratoire de Biochimie Th\u00e9orique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cit\u00e9, F-75005 Paris, France and 2Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I169173203","https://openalex.org/I204730241","https://openalex.org/I40120149","https://openalex.org/I4210091437","https://openalex.org/I4210094297"]},{"raw_affiliation_string":"LBT (UPR_9080) - Laboratoire de biochimie th\u00e9orique [Paris] (13 Rue Pierre et Marie Curie 75005 PARIS - France)","institution_ids":["https://openalex.org/I4210094297"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111406166","display_name":"Anna Caroline E. Dahl","orcid":null},"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/I169173203","display_name":"D\u00e9l\u00e9gation Paris 7","ror":"https://ror.org/00bw5n526","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488","https://openalex.org/I169173203"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210091437","display_name":"Sorbonne Paris Cit\u00e9","ror":"https://ror.org/001z21q04","country_code":"FR","type":"other","lineage":["https://openalex.org/I4210091437"]},{"id":"https://openalex.org/I4210094297","display_name":"Laboratoire de Biochimie Th\u00e9orique","ror":"https://ror.org/00nvjgv40","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4210094297","https://openalex.org/I4210128300"]}],"countries":["FR","GB"],"is_corresponding":false,"raw_author_name":"Anna Caroline E. Dahl","raw_affiliation_strings":["1 Laboratoire de Biochimie Th\u00e9orique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cit\u00e9, F-75005 Paris, France and 2Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK","SBCB - Structural Bioinformatics and Computational Biochemistry [Oxford] (University of Oxford\r\nSouth Parks Road\r\nOxford OX1 3QU - United Kingdom)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Laboratoire de Biochimie Th\u00e9orique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cit\u00e9, F-75005 Paris, France and 2Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I169173203","https://openalex.org/I204730241","https://openalex.org/I40120149","https://openalex.org/I4210091437","https://openalex.org/I4210094297"]},{"raw_affiliation_string":"SBCB - Structural Bioinformatics and Computational Biochemistry [Oxford] (University of Oxford\r\nSouth Parks Road\r\nOxford OX1 3QU - United Kingdom)","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062848902","display_name":"Samuela Pasquali","orcid":"https://orcid.org/0000-0003-1487-0894"},"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/I169173203","display_name":"D\u00e9l\u00e9gation Paris 7","ror":"https://ror.org/00bw5n526","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488","https://openalex.org/I169173203"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210091437","display_name":"Sorbonne Paris Cit\u00e9","ror":"https://ror.org/001z21q04","country_code":"FR","type":"other","lineage":["https://openalex.org/I4210091437"]},{"id":"https://openalex.org/I4210094297","display_name":"Laboratoire de Biochimie Th\u00e9orique","ror":"https://ror.org/00nvjgv40","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4210094297","https://openalex.org/I4210128300"]}],"countries":["FR","GB"],"is_corresponding":false,"raw_author_name":"Samuela Pasquali","raw_affiliation_strings":["1 Laboratoire de Biochimie Th\u00e9orique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cit\u00e9, F-75005 Paris, France and 2Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK","LBT (UPR_9080) - Laboratoire de biochimie th\u00e9orique [Paris] (13 Rue Pierre et Marie Curie 75005 PARIS - France)","Universite\u0301 Paris Diderot, Sorbonne Paris Cite\u0301, Paris, France (France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Laboratoire de Biochimie Th\u00e9orique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cit\u00e9, F-75005 Paris, France and 2Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I169173203","https://openalex.org/I204730241","https://openalex.org/I40120149","https://openalex.org/I4210091437","https://openalex.org/I4210094297"]},{"raw_affiliation_string":"LBT (UPR_9080) - Laboratoire de biochimie th\u00e9orique [Paris] (13 Rue Pierre et Marie Curie 75005 PARIS - France)","institution_ids":["https://openalex.org/I4210094297"]},{"raw_affiliation_string":"Universite\u0301 Paris Diderot, Sorbonne Paris Cite\u0301, Paris, France (France)","institution_ids":["https://openalex.org/I169173203","https://openalex.org/I204730241","https://openalex.org/I4210091437"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090416900","display_name":"Philippe Derreumaux","orcid":"https://orcid.org/0000-0001-9110-5585"},"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/I169173203","display_name":"D\u00e9l\u00e9gation Paris 7","ror":"https://ror.org/00bw5n526","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488","https://openalex.org/I169173203"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210091437","display_name":"Sorbonne Paris Cit\u00e9","ror":"https://ror.org/001z21q04","country_code":"FR","type":"other","lineage":["https://openalex.org/I4210091437"]},{"id":"https://openalex.org/I4210094297","display_name":"Laboratoire de Biochimie Th\u00e9orique","ror":"https://ror.org/00nvjgv40","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4210094297","https://openalex.org/I4210128300"]}],"countries":["FR","GB"],"is_corresponding":false,"raw_author_name":"Philippe Derreumaux","raw_affiliation_strings":["1 Laboratoire de Biochimie Th\u00e9orique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cit\u00e9, F-75005 Paris, France and 2Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK","LBT (UPR_9080) - Laboratoire de biochimie th\u00e9orique [Paris] (13 Rue Pierre et Marie Curie 75005 PARIS - France)","Universite\u0301 Paris Diderot, Sorbonne Paris Cite\u0301, Paris, France (France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Laboratoire de Biochimie Th\u00e9orique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cit\u00e9, F-75005 Paris, France and 2Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I169173203","https://openalex.org/I204730241","https://openalex.org/I40120149","https://openalex.org/I4210091437","https://openalex.org/I4210094297"]},{"raw_affiliation_string":"LBT (UPR_9080) - Laboratoire de biochimie th\u00e9orique [Paris] (13 Rue Pierre et Marie Curie 75005 PARIS - France)","institution_ids":["https://openalex.org/I4210094297"]},{"raw_affiliation_string":"Universite\u0301 Paris Diderot, Sorbonne Paris Cite\u0301, Paris, France (France)","institution_ids":["https://openalex.org/I169173203","https://openalex.org/I204730241","https://openalex.org/I4210091437"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041718990","display_name":"Mark S.P. Sansom","orcid":"https://orcid.org/0000-0001-6360-7959"},"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/I169173203","display_name":"D\u00e9l\u00e9gation Paris 7","ror":"https://ror.org/00bw5n526","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488","https://openalex.org/I169173203"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210091437","display_name":"Sorbonne Paris Cit\u00e9","ror":"https://ror.org/001z21q04","country_code":"FR","type":"other","lineage":["https://openalex.org/I4210091437"]},{"id":"https://openalex.org/I4210094297","display_name":"Laboratoire de Biochimie Th\u00e9orique","ror":"https://ror.org/00nvjgv40","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4210094297","https://openalex.org/I4210128300"]}],"countries":["FR","GB"],"is_corresponding":false,"raw_author_name":"Mark S.P. Sansom","raw_affiliation_strings":["1 Laboratoire de Biochimie Th\u00e9orique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cit\u00e9, F-75005 Paris, France and 2Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK","SBCB - Structural Bioinformatics and Computational Biochemistry [Oxford] (University of Oxford\r\nSouth Parks Road\r\nOxford OX1 3QU - United Kingdom)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Laboratoire de Biochimie Th\u00e9orique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cit\u00e9, F-75005 Paris, France and 2Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I169173203","https://openalex.org/I204730241","https://openalex.org/I40120149","https://openalex.org/I4210091437","https://openalex.org/I4210094297"]},{"raw_affiliation_string":"SBCB - Structural Bioinformatics and Computational Biochemistry [Oxford] (University of Oxford\r\nSouth Parks Road\r\nOxford OX1 3QU - United Kingdom)","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016139627","display_name":"Marc Baaden","orcid":"https://orcid.org/0000-0001-6472-0486"},"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/I169173203","display_name":"D\u00e9l\u00e9gation Paris 7","ror":"https://ror.org/00bw5n526","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488","https://openalex.org/I169173203"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210091437","display_name":"Sorbonne Paris Cit\u00e9","ror":"https://ror.org/001z21q04","country_code":"FR","type":"other","lineage":["https://openalex.org/I4210091437"]},{"id":"https://openalex.org/I4210094297","display_name":"Laboratoire de Biochimie Th\u00e9orique","ror":"https://ror.org/00nvjgv40","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4210094297","https://openalex.org/I4210128300"]}],"countries":["FR","GB"],"is_corresponding":true,"raw_author_name":"Marc Baaden","raw_affiliation_strings":["1 Laboratoire de Biochimie Th\u00e9orique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cit\u00e9, F-75005 Paris, France and 2Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK","LBT (UPR_9080) - Laboratoire de biochimie th\u00e9orique [Paris] (13 Rue Pierre et Marie Curie 75005 PARIS - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Laboratoire de Biochimie Th\u00e9orique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cit\u00e9, F-75005 Paris, France and 2Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I169173203","https://openalex.org/I204730241","https://openalex.org/I40120149","https://openalex.org/I4210091437","https://openalex.org/I4210094297"]},{"raw_affiliation_string":"LBT (UPR_9080) - Laboratoire de biochimie th\u00e9orique [Paris] (13 Rue Pierre et Marie Curie 75005 PARIS - France)","institution_ids":["https://openalex.org/I4210094297"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5016139627","https://openalex.org/A5020115791"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I169173203","https://openalex.org/I204730241","https://openalex.org/I40120149","https://openalex.org/I4210091437","https://openalex.org/I4210094297"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":1530,"currency":"EUR","value_usd":1650},"fwci":2.4697,"has_fulltext":false,"cited_by_count":118,"citation_normalized_percentile":{"value":0.89776068,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"31","issue":"9","first_page":"1478","last_page":"1480"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.553600013256073,"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":0.553600013256073,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.08380000293254852,"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":0.07819999754428864,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8921968936920166},{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.8886657953262329},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7722103595733643},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.7515732049942017},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6079659461975098},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.579245388507843},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5788701772689819},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5591558218002319},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5193892121315002},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.40109479427337646}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8921968936920166},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.8886657953262329},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7722103595733643},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.7515732049942017},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6079659461975098},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.579245388507843},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5788701772689819},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5591558218002319},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5193892121315002},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.40109479427337646},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007473","descriptor_name":"Ion Channels","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D007473","descriptor_name":"Ion Channels","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D007473","descriptor_name":"Ion Channels","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D007473","descriptor_name":"Ion Channels","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D007473","descriptor_name":"Ion Channels","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D007473","descriptor_name":"Ion Channels","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018841","descriptor_name":"HSP90 Heat-Shock Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018841","descriptor_name":"HSP90 Heat-Shock Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018841","descriptor_name":"HSP90 Heat-Shock Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018841","descriptor_name":"HSP90 Heat-Shock Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018841","descriptor_name":"HSP90 Heat-Shock Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018841","descriptor_name":"HSP90 Heat-Shock Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":5,"locations":[{"id":"doi:10.1093/bioinformatics/btu822","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu822","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/9/1478/17085621/btu822.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25505095","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25505095","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-01230764v1","is_oa":false,"landing_page_url":"https://hal.science/hal-01230764","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":"Bioinformatics, 2015, 31 (9), pp.1478-1480. ⟨10.1093/bioinformatics/btu822⟩","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:oskar-bordeaux.fr:20.500.12278/113999","is_oa":false,"landing_page_url":"https://oskar-bordeaux.fr/handle/20.500.12278/113999","pdf_url":null,"source":{"id":"https://openalex.org/S4306402569","display_name":"Oskar-Bordeaux (Universite de Bordeaux)","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":"","raw_type":"Article de revue"},{"id":"pmh:oai:pubmedcentral.nih.gov:4410650","is_oa":true,"landing_page_url":"http://doi.org/10.1093/bioinformatics/btu822","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu822","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu822","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/9/1478/17085621/btu822.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2297262676","display_name":"Exa-scalable interactive visual analysis for life & materials sciences","funder_award_id":"ANR-11-MONU-0003","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G3409323988","display_name":"Structural characterization of both closed and open forms of a ligand-gated ion channel of the cys-loop family and molecular mechanism of the transition","funder_award_id":"ANR-10-BLAN-1534","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G8924954789","display_name":"Dynamique des membranes transductrices d'\u00e9nergie : biog\u00e9n\u00e8se et organisation supramol\u00e9culaire.","funder_award_id":"ANR-11-LABX-0011","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2107278499.pdf"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W2020288705","https://openalex.org/W2029667189","https://openalex.org/W2052773080","https://openalex.org/W2101532349","https://openalex.org/W2113007147","https://openalex.org/W2158076215","https://openalex.org/W2334874683"],"related_works":["https://openalex.org/W3023169329","https://openalex.org/W4389470870","https://openalex.org/W2782165897","https://openalex.org/W1582950852","https://openalex.org/W4300438041","https://openalex.org/W2093416473","https://openalex.org/W2054104202","https://openalex.org/W2139703748","https://openalex.org/W2761254753","https://openalex.org/W1024825291"],"abstract_inverted_index":{"SUMMARY:":[0],"The":[1],"volume":[2],"of":[3,32],"an":[4,38],"internal":[5],"protein":[6],"pocket":[7,44],"is":[8],"fundamental":[9],"to":[10,60],"ligand":[11],"accessibility.":[12],"Few":[13],"programs":[14],"that":[15,42],"compute":[16],"such":[17],"volumes":[18,45],"manage":[19],"dynamic":[20],"data":[21,99],"from":[22,46],"molecular":[23],"dynamics":[24],"(MD)":[25],"simulations.":[26],"Limited":[27],"performance":[28],"often":[29],"prohibits":[30],"analysis":[31,78],"large":[33],"datasets.":[34],"We":[35],"present":[36],"Epock,":[37],"efficient":[39],"command-line":[40],"tool":[41],"calculates":[43],"MD":[47],"trajectories.":[48],"A":[49],"plugin":[50],"for":[51],"the":[52,68],"VMD":[53,80],"program":[54],"provides":[55],"a":[56],"graphical":[57],"user":[58],"interface":[59],"facilitate":[61],"input":[62],"creation,":[63],"run":[64],"Epock":[65,73],"and":[66,84],"analyse":[67],"results.":[69],"AVAILABILITY":[70],"AND":[71],"IMPLEMENTATION:":[72],"C++":[74],"source":[75],"code,":[76],"Python":[77],"scripts,":[79],"Tcl":[81],"plugin,":[82],"documentation":[83],"installation":[85],"instructions":[86],"are":[87,100],"freely":[88],"available":[89,101],"at":[90,102],"http://epock.bitbucket.org.":[91],"CONTACT:":[92],"benoist.laurent@gmail.com":[93],"or":[94],"baaden@smplinux.de":[95],"SUPPLEMENTARY":[96],"INFORMATION:":[97],"Supplementary":[98],"Bioinformatics":[103],"online.":[104]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":16},{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":16},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":12},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":12},{"year":2016,"cited_by_count":7}],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2025-10-10T00:00:00"}