{"id":"https://openalex.org/W4399849772","doi":"https://doi.org/10.1371/journal.pcbi.1012173","title":"Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows","display_name":"Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows","publication_year":2024,"publication_date":"2024-06-20","ids":{"openalex":"https://openalex.org/W4399849772","doi":"https://doi.org/10.1371/journal.pcbi.1012173","pmid":"https://pubmed.ncbi.nlm.nih.gov/38900779"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1012173","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012173","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012173&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012173&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091460370","display_name":"Gen\u00eds Bayarri","orcid":"https://orcid.org/0000-0003-0513-0288"},"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"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Gen\u00eds Bayarri","raw_affiliation_strings":["Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain","institution_ids":["https://openalex.org/I4210122345"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051114531","display_name":"Pau Andrio","orcid":"https://orcid.org/0000-0003-2116-3880"},"institutions":[{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"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":"Pau Andrio","raw_affiliation_strings":["Barcelona Supercomputing Center (BSC), Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center (BSC), Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088134705","display_name":"Josep Llu\u00eds Gelp\u00ed","orcid":"https://orcid.org/0000-0002-0566-7723"},"institutions":[{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"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":"Josep Llu\u00eds Gelp\u00ed","raw_affiliation_strings":["Barcelona Supercomputing Center (BSC), Barcelona, Spain","Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center (BSC), Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]},{"raw_affiliation_string":"Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona, Spain","institution_ids":["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"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Modesto Orozco","raw_affiliation_strings":["Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona, Spain","Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona, Spain","institution_ids":["https://openalex.org/I71999127"]},{"raw_affiliation_string":"Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain","institution_ids":["https://openalex.org/I4210122345"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5006399866","https://openalex.org/A5051114531","https://openalex.org/A5088134705","https://openalex.org/A5091460370"],"corresponding_institution_ids":["https://openalex.org/I2799803557","https://openalex.org/I4210122345","https://openalex.org/I71999127","https://openalex.org/I9617848"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.02,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.84940004,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"20","issue":"6","first_page":"e1012173","last_page":"e1012173"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11937","display_name":"Research Data Management Practices","score":0.9847999811172485,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9696000218391418,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/workflow","display_name":"Workflow","score":0.856931746006012},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7962214350700378},{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.6851157546043396},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6684023141860962},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5970497727394104},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.47573399543762207},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.4173596203327179},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3621164858341217},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3150259852409363},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2470291554927826},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.21778380870819092},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.13544431328773499}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.856931746006012},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7962214350700378},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.6851157546043396},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6684023141860962},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5970497727394104},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.47573399543762207},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.4173596203327179},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3621164858341217},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3150259852409363},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2470291554927826},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.21778380870819092},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.13544431328773499},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0}],"mesh":[{"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":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1012173","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012173","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012173&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:38900779","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38900779","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:upcommons.upc.edu:2117/413104","is_oa":true,"landing_page_url":"https://hdl.handle.net/2117/413104","pdf_url":"https://upcommons.upc.edu/bitstreams/ac398698-79d1-458d-b881-62e2f62999c2/download","source":{"id":"https://openalex.org/S4210207057","display_name":"QRU Quaderns de Recerca en Urbanisme","issn_l":"2014-9689","issn":["2014-9689","2385-6777"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310322448","host_organization_name":"Q71272178","host_organization_lineage":["https://openalex.org/P4310322448"],"host_organization_lineage_names":["Q71272178"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11189206","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11189206","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11189206/pdf/pcbi.1012173.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:3d06dcac195746eab6375d2b780d6aec","is_oa":true,"landing_page_url":"https://doaj.org/article/3d06dcac195746eab6375d2b780d6aec","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 20, Iss 6, p e1012173 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1012173","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012173","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012173&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.800000011920929}],"awards":[{"id":"https://openalex.org/G1333925561","display_name":null,"funder_award_id":"101094651","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G1577988765","display_name":null,"funder_award_id":"823830","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G2502897618","display_name":null,"funder_award_id":"SGR2021 00863","funder_id":"https://openalex.org/F4320334830","funder_display_name":"Ag\u00e8ncia de Gesti\u00f3 d'Ajuts Universitaris i de Recerca"},{"id":"https://openalex.org/G2558159905","display_name":null,"funder_award_id":"17/0009/0007","funder_id":"https://openalex.org/F4320334923","funder_display_name":"Instituto de Salud Carlos III"},{"id":"https://openalex.org/G3471917844","display_name":null,"funder_award_id":"823830","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G3514550006","display_name":null,"funder_award_id":"Centre","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6133374110","display_name":null,"funder_award_id":"ISCIII PT 17/0009/0007","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G6298273575","display_name":null,"funder_award_id":"RTI2018","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G6630833806","display_name":null,"funder_award_id":"101093290","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6719859577","display_name":null,"funder_award_id":"SGR2021 00863","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G6846970787","display_name":null,"funder_award_id":"ISCIII PT 17/0009/0007","funder_id":"https://openalex.org/F4320334923","funder_display_name":"Instituto de Salud Carlos III"},{"id":"https://openalex.org/G8570012161","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320334830","display_name":"Ag\u00e8ncia de Gesti\u00f3 d'Ajuts Universitaris i de Recerca","ror":"https://ror.org/01n4pqe45"},{"id":"https://openalex.org/F4320334923","display_name":"Instituto de Salud Carlos III","ror":"https://ror.org/00ca2c886"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4399849772.pdf"},"referenced_works_count":62,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1168671556","https://openalex.org/W1965932123","https://openalex.org/W2008985174","https://openalex.org/W2011301426","https://openalex.org/W2018518196","https://openalex.org/W2074400988","https://openalex.org/W2112712631","https://openalex.org/W2114850508","https://openalex.org/W2130479394","https://openalex.org/W2132589721","https://openalex.org/W2134967712","https://openalex.org/W2140047797","https://openalex.org/W2141541659","https://openalex.org/W2145374174","https://openalex.org/W2164088236","https://openalex.org/W2302501749","https://openalex.org/W2342674011","https://openalex.org/W2346143774","https://openalex.org/W2472803348","https://openalex.org/W2474648852","https://openalex.org/W2539403003","https://openalex.org/W2570760970","https://openalex.org/W2765745983","https://openalex.org/W2772099288","https://openalex.org/W2806399642","https://openalex.org/W2900830509","https://openalex.org/W2911094364","https://openalex.org/W2952768760","https://openalex.org/W2972751083","https://openalex.org/W2974666250","https://openalex.org/W2986579771","https://openalex.org/W3006277460","https://openalex.org/W3013954280","https://openalex.org/W3015598776","https://openalex.org/W3054029144","https://openalex.org/W3095077518","https://openalex.org/W3141677440","https://openalex.org/W3155944610","https://openalex.org/W3157788795","https://openalex.org/W3208217019","https://openalex.org/W3215553101","https://openalex.org/W4220806817","https://openalex.org/W4220810573","https://openalex.org/W4224282974","https://openalex.org/W4229064944","https://openalex.org/W4281688690","https://openalex.org/W4282918903","https://openalex.org/W4285773620","https://openalex.org/W4294000869","https://openalex.org/W4295905006","https://openalex.org/W4306173528","https://openalex.org/W4312044861","https://openalex.org/W4312226430","https://openalex.org/W4377010480","https://openalex.org/W4387129847","https://openalex.org/W6729352201","https://openalex.org/W6910314935","https://openalex.org/W6929298704","https://openalex.org/W6948177337","https://openalex.org/W6948291833","https://openalex.org/W6982728064"],"related_works":["https://openalex.org/W2093262417","https://openalex.org/W2618286804","https://openalex.org/W2123131699","https://openalex.org/W2329643025","https://openalex.org/W650116260","https://openalex.org/W2378329187","https://openalex.org/W4390790060","https://openalex.org/W2134191509","https://openalex.org/W3209454962","https://openalex.org/W79697243"],"abstract_inverted_index":{"Interactive":[0],"Jupyter":[1],"Notebooks":[2],"in":[3,47,101],"combination":[4],"with":[5,36,96,124],"Conda":[6],"environments":[7],"can":[8,93],"be":[9,53,94],"used":[10],"to":[11,32,55,110],"generate":[12],"FAIR":[13,67],"(Findable,":[14],"Accessible,":[15],"Interoperable":[16],"and":[17,29,40,88,117,122,129],"Reusable/Reproducible)":[18],"biomolecular":[19,74],"simulation":[20,75],"workflows.":[21],"The":[22,105],"interactive":[23],"programming":[24],"code":[25],"accompanied":[26],"by":[27],"documentation":[28],"the":[30,73],"possibility":[31],"inspect":[33],"intermediate":[34],"results":[35],"versatile":[37],"graphical":[38],"charts":[39],"data":[41],"visualization":[42],"is":[43,119],"very":[44],"helpful,":[45],"especially":[46],"iterative":[48],"processes,":[49],"where":[50],"parameters":[51],"might":[52],"adjusted":[54],"a":[56,64,102,112],"particular":[57],"system":[58],"of":[59,66,72,107,114],"interest.":[60],"This":[61],"work":[62],"presents":[63],"collection":[65,106],"notebooks":[68,108],"covering":[69],"various":[70],"areas":[71],"field,":[76],"such":[77],"as":[78],"molecular":[79,84,86],"dynamics":[80],"(MD),":[81],"protein-ligand":[82],"docking,":[83],"checking/modeling,":[85],"interactions,":[87],"free":[89],"energy":[90],"perturbations.":[91],"Workflows":[92],"launched":[95],"myBinder":[97],"or":[98],"easily":[99],"installed":[100],"local":[103],"system.":[104],"aims":[109],"provide":[111],"compilation":[113],"demonstration":[115],"workflows,":[116],"it":[118],"continuously":[120],"updated":[121],"expanded":[123],"examples":[125],"using":[126],"new":[127],"methodologies":[128],"tools.":[130]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
