{"id":"https://openalex.org/W2749780981","doi":"https://doi.org/10.1093/bioinformatics/btx529","title":"Integrative structural and dynamical biology with PLUMED-ISDB","display_name":"Integrative structural and dynamical biology with PLUMED-ISDB","publication_year":2017,"publication_date":"2017-08-17","ids":{"openalex":"https://openalex.org/W2749780981","doi":"https://doi.org/10.1093/bioinformatics/btx529","mag":"2749780981","pmid":"https://pubmed.ncbi.nlm.nih.gov/28961689"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx529","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx529","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/24/3999/25168471/btx529.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/33/24/3999/25168471/btx529.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056483461","display_name":"Massimiliano Bonomi","orcid":"https://orcid.org/0000-0002-7321-0004"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Massimiliano Bonomi","raw_affiliation_strings":["Department of Chemistry, University of Cambridge, Cambridge, UK"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Cambridge, Cambridge, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044583992","display_name":"Carlo Camilloni","orcid":"https://orcid.org/0000-0002-9923-8590"},"institutions":[{"id":"https://openalex.org/I189158943","display_name":"University of Milan","ror":"https://ror.org/00wjc7c48","country_code":"IT","type":"education","lineage":["https://openalex.org/I189158943"]},{"id":"https://openalex.org/I4210137766","display_name":"Institute for Advanced Study","ror":"https://ror.org/03xg85719","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210137766"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE","IT"],"is_corresponding":true,"raw_author_name":"Carlo Camilloni","raw_affiliation_strings":["Department of Chemistry, Institute for Advanced Study, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","Dipartimento di Bioscienze, Universit\u00e0 degli Studi di Milano, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Institute for Advanced Study, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","institution_ids":["https://openalex.org/I62916508","https://openalex.org/I4210137766"]},{"raw_affiliation_string":"Dipartimento di Bioscienze, Universit\u00e0 degli Studi di Milano, Milan, Italy","institution_ids":["https://openalex.org/I189158943"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5044583992","https://openalex.org/A5056483461"],"corresponding_institution_ids":["https://openalex.org/I189158943","https://openalex.org/I241749","https://openalex.org/I4210137766","https://openalex.org/I62916508"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":4.6029,"has_fulltext":true,"cited_by_count":84,"citation_normalized_percentile":{"value":0.95764719,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"33","issue":"24","first_page":"3999","last_page":"4000"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9919999837875366,"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":0.9897000193595886,"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/computer-science","display_name":"Computer science","score":0.6478567123413086},{"id":"https://openalex.org/keywords/a-priori-and-a-posteriori","display_name":"A priori and a posteriori","score":0.5299488306045532},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4230431914329529},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40876415371894836},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1824226677417755}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6478567123413086},{"id":"https://openalex.org/C75553542","wikidata":"https://www.wikidata.org/wiki/Q178161","display_name":"A priori and a posteriori","level":2,"score":0.5299488306045532},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4230431914329529},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40876415371894836},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1824226677417755},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btx529","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx529","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/24/3999/25168471/btx529.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:28961689","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28961689","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:air.unimi.it:2434/543164","is_oa":true,"landing_page_url":"http://hdl.handle.net/2434/543164","pdf_url":"https://air.unimi.it/bitstream/2434/543164/2/plumed-ISDB%20revised.pdf","source":{"id":"https://openalex.org/S4306400516","display_name":"Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I189158943","host_organization_name":"University of Milan","host_organization_lineage":["https://openalex.org/I189158943"],"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":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:HAL:hal-03136441v1","is_oa":true,"landing_page_url":"https://hal.science/hal-03136441","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, 2017, 33 (24), pp.3999-4000. &#x27E8;10.1093/bioinformatics/btx529&#x27E9;","raw_type":"Journal articles"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx529","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx529","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/24/3999/25168471/btx529.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/G8345540293","display_name":null,"funder_award_id":"291763","funder_id":"https://openalex.org/F4320323383","funder_display_name":"Technische Universit\u00e4t M\u00fcnchen"}],"funders":[{"id":"https://openalex.org/F4320323383","display_name":"Technische Universit\u00e4t M\u00fcnchen","ror":"https://ror.org/02kkvpp62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2749780981.pdf","grobid_xml":"https://content.openalex.org/works/W2749780981.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1998177378","https://openalex.org/W2008850469","https://openalex.org/W2051091550","https://openalex.org/W2129821632","https://openalex.org/W2146411229","https://openalex.org/W2265101181","https://openalex.org/W2512849379","https://openalex.org/W2570104014","https://openalex.org/W2594784077","https://openalex.org/W2608491550","https://openalex.org/W3019931530","https://openalex.org/W6735010452"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4388311650","https://openalex.org/W5922282","https://openalex.org/W1974056099","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4245343541"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":15},{"year":2018,"cited_by_count":12},{"year":2017,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
