{"id":"https://openalex.org/W2171002664","doi":"https://doi.org/10.1093/bioinformatics/btt324","title":"Exploration of conformational transition pathways from coarse-grained simulations","display_name":"Exploration of conformational transition pathways from coarse-grained simulations","publication_year":2013,"publication_date":"2013-06-05","ids":{"openalex":"https://openalex.org/W2171002664","doi":"https://doi.org/10.1093/bioinformatics/btt324","mag":"2171002664","pmid":"https://pubmed.ncbi.nlm.nih.gov/23740746"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt324","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt324","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/16/1980/49076829/bioinformatics_29_16_1980.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/29/16/1980/49076829/bioinformatics_29_16_1980.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009300970","display_name":"Pedro Sfriso","orcid":null},"institutions":[{"id":"https://openalex.org/I4210122345","display_name":"Institute for Research in Biomedicine","ror":"https://ror.org/01z1gye03","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210122345","https://openalex.org/I4210132884","https://openalex.org/I4387153040"]},{"id":"https://openalex.org/I71999127","display_name":"Universitat de Barcelona","ror":"https://ror.org/021018s57","country_code":"ES","type":"education","lineage":["https://openalex.org/I71999127"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Pedro Sfriso","raw_affiliation_strings":["1 Institute for Research in Biomedicine (IRB Barcelona), 2Joint IRB-BSC Program in Computational Biology, Baldiri Reixac 10, Barcelona 08028, Spain, 3National Institute of Bioinformatics and 4Department of Biochemistry and Molecular Biology, University of Barcelona, Av. Diagonal 647, Barcelona 08028, Spain"],"affiliations":[{"raw_affiliation_string":"1 Institute for Research in Biomedicine (IRB Barcelona), 2Joint IRB-BSC Program in Computational Biology, Baldiri Reixac 10, Barcelona 08028, Spain, 3National Institute of Bioinformatics and 4Department of Biochemistry and Molecular Biology, University of Barcelona, Av. Diagonal 647, Barcelona 08028, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I4210122345","https://openalex.org/I71999127"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058831119","display_name":"Agust\u00ed Emperador","orcid":"https://orcid.org/0000-0002-8441-1821"},"institutions":[{"id":"https://openalex.org/I4210122345","display_name":"Institute for Research in Biomedicine","ror":"https://ror.org/01z1gye03","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210122345","https://openalex.org/I4210132884","https://openalex.org/I4387153040"]},{"id":"https://openalex.org/I71999127","display_name":"Universitat de Barcelona","ror":"https://ror.org/021018s57","country_code":"ES","type":"education","lineage":["https://openalex.org/I71999127"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Agust\u00ed Emperador","raw_affiliation_strings":["1 Institute for Research in Biomedicine (IRB Barcelona), 2Joint IRB-BSC Program in Computational Biology, Baldiri Reixac 10, Barcelona 08028, Spain, 3National Institute of Bioinformatics and 4Department of Biochemistry and Molecular Biology, University of Barcelona, Av. Diagonal 647, Barcelona 08028, Spain"],"affiliations":[{"raw_affiliation_string":"1 Institute for Research in Biomedicine (IRB Barcelona), 2Joint IRB-BSC Program in Computational Biology, Baldiri Reixac 10, Barcelona 08028, Spain, 3National Institute of Bioinformatics and 4Department of Biochemistry and Molecular Biology, University of Barcelona, Av. Diagonal 647, Barcelona 08028, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I4210122345","https://openalex.org/I71999127"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006399866","display_name":"Modesto Orozco","orcid":"https://orcid.org/0000-0002-8608-3278"},"institutions":[{"id":"https://openalex.org/I4210122345","display_name":"Institute for Research in Biomedicine","ror":"https://ror.org/01z1gye03","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210122345","https://openalex.org/I4210132884","https://openalex.org/I4387153040"]},{"id":"https://openalex.org/I71999127","display_name":"Universitat de Barcelona","ror":"https://ror.org/021018s57","country_code":"ES","type":"education","lineage":["https://openalex.org/I71999127"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Modesto Orozco","raw_affiliation_strings":["1 Institute for Research in Biomedicine (IRB Barcelona), 2Joint IRB-BSC Program in Computational Biology, Baldiri Reixac 10, Barcelona 08028, Spain, 3National Institute of Bioinformatics and 4Department of Biochemistry and Molecular Biology, University of Barcelona, Av. Diagonal 647, Barcelona 08028, Spain"],"affiliations":[{"raw_affiliation_string":"1 Institute for Research in Biomedicine (IRB Barcelona), 2Joint IRB-BSC Program in Computational Biology, Baldiri Reixac 10, Barcelona 08028, Spain, 3National Institute of Bioinformatics and 4Department of Biochemistry and Molecular Biology, University of Barcelona, Av. Diagonal 647, Barcelona 08028, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I4210122345","https://openalex.org/I71999127"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5009300970"],"corresponding_institution_ids":["https://openalex.org/I4210122345","https://openalex.org/I71999127","https://openalex.org/I9617848"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.0964,"has_fulltext":true,"cited_by_count":31,"citation_normalized_percentile":{"value":0.87416855,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"29","issue":"16","first_page":"1980","last_page":"1986"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9983000159263611,"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":0.9957000017166138,"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/metadynamics","display_name":"Metadynamics","score":0.8823971152305603},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.7307108044624329},{"id":"https://openalex.org/keywords/maxima-and-minima","display_name":"Maxima and minima","score":0.6807907819747925},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6185270547866821},{"id":"https://openalex.org/keywords/trace","display_name":"TRACE (psycholinguistics)","score":0.5725946426391602},{"id":"https://openalex.org/keywords/energy-landscape","display_name":"Energy landscape","score":0.4949492812156677},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.44733768701553345},{"id":"https://openalex.org/keywords/conformational-ensembles","display_name":"Conformational ensembles","score":0.4422316253185272},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.42405208945274353},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.4194607734680176},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.33660995960235596},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3308638036251068},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.31350886821746826},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.25886815786361694},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.13623669743537903},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09737592935562134}],"concepts":[{"id":"https://openalex.org/C62752575","wikidata":"https://www.wikidata.org/wiki/Q6822487","display_name":"Metadynamics","level":3,"score":0.8823971152305603},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7307108044624329},{"id":"https://openalex.org/C186633575","wikidata":"https://www.wikidata.org/wiki/Q845060","display_name":"Maxima and minima","level":2,"score":0.6807907819747925},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6185270547866821},{"id":"https://openalex.org/C75291252","wikidata":"https://www.wikidata.org/wiki/Q1315756","display_name":"TRACE (psycholinguistics)","level":2,"score":0.5725946426391602},{"id":"https://openalex.org/C119621388","wikidata":"https://www.wikidata.org/wiki/Q5377166","display_name":"Energy landscape","level":2,"score":0.4949492812156677},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.44733768701553345},{"id":"https://openalex.org/C2777936996","wikidata":"https://www.wikidata.org/wiki/Q17148461","display_name":"Conformational ensembles","level":3,"score":0.4422316253185272},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.42405208945274353},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.4194607734680176},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.33660995960235596},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3308638036251068},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.31350886821746826},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.25886815786361694},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.13623669743537903},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09737592935562134},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","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":"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":2,"locations":[{"id":"doi:10.1093/bioinformatics/btt324","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt324","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/16/1980/49076829/bioinformatics_29_16_1980.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:23740746","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23740746","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt324","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt324","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/16/1980/49076829/bioinformatics_29_16_1980.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":[{"score":0.800000011920929,"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322121","display_name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats","ror":"https://ror.org/0371hy230"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2171002664.pdf","grobid_xml":"https://content.openalex.org/works/W2171002664.grobid-xml"},"referenced_works_count":72,"referenced_works":["https://openalex.org/W1536379485","https://openalex.org/W1550166367","https://openalex.org/W1582833325","https://openalex.org/W1965814986","https://openalex.org/W1969723894","https://openalex.org/W1970454429","https://openalex.org/W1974225312","https://openalex.org/W1987104859","https://openalex.org/W1992192767","https://openalex.org/W1995717154","https://openalex.org/W1998367993","https://openalex.org/W2000670326","https://openalex.org/W2004577830","https://openalex.org/W2010956452","https://openalex.org/W2014095962","https://openalex.org/W2014425795","https://openalex.org/W2015059998","https://openalex.org/W2016819659","https://openalex.org/W2019493938","https://openalex.org/W2028806001","https://openalex.org/W2031340110","https://openalex.org/W2047346757","https://openalex.org/W2049598343","https://openalex.org/W2053893146","https://openalex.org/W2057126467","https://openalex.org/W2057594534","https://openalex.org/W2058206198","https://openalex.org/W2066961392","https://openalex.org/W2067204014","https://openalex.org/W2067236515","https://openalex.org/W2067763399","https://openalex.org/W2077412035","https://openalex.org/W2078062549","https://openalex.org/W2079199763","https://openalex.org/W2079875740","https://openalex.org/W2082028745","https://openalex.org/W2084258253","https://openalex.org/W2091752317","https://openalex.org/W2099490136","https://openalex.org/W2102099014","https://openalex.org/W2105254477","https://openalex.org/W2106393249","https://openalex.org/W2107268733","https://openalex.org/W2109987496","https://openalex.org/W2110534399","https://openalex.org/W2114320488","https://openalex.org/W2119267663","https://openalex.org/W2119822484","https://openalex.org/W2120781005","https://openalex.org/W2121400889","https://openalex.org/W2122326469","https://openalex.org/W2124929769","https://openalex.org/W2127362915","https://openalex.org/W2134528197","https://openalex.org/W2142012138","https://openalex.org/W2142595184","https://openalex.org/W2142694980","https://openalex.org/W2144857097","https://openalex.org/W2149655632","https://openalex.org/W2149744037","https://openalex.org/W2149954732","https://openalex.org/W2157182791","https://openalex.org/W2157467256","https://openalex.org/W2160338718","https://openalex.org/W2160349767","https://openalex.org/W2161151688","https://openalex.org/W2164548935","https://openalex.org/W2165845608","https://openalex.org/W2171144241","https://openalex.org/W2323759742","https://openalex.org/W2327425795","https://openalex.org/W3106205370"],"related_works":["https://openalex.org/W2124175595","https://openalex.org/W2147022472","https://openalex.org/W2035527380","https://openalex.org/W4306735371","https://openalex.org/W1977626220","https://openalex.org/W2144674873","https://openalex.org/W1976698905","https://openalex.org/W4220878319","https://openalex.org/W2063945425","https://openalex.org/W3136571708"],"abstract_inverted_index":{"Freely":[0],"available":[1],"on":[2],"the":[3],"web":[4],"at":[5],"http://mmb.irbbarcelona.org/GOdMD.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-11T08:14:18.477133","created_date":"2025-10-10T00:00:00"}
