{"id":"https://openalex.org/W4415462938","doi":"https://doi.org/10.1186/s13321-025-01082-5","title":"Gromacs MetaDump: a tool for extracting GROMACS simulation metadata","display_name":"Gromacs MetaDump: a tool for extracting GROMACS simulation metadata","publication_year":2025,"publication_date":"2025-10-23","ids":{"openalex":"https://openalex.org/W4415462938","doi":"https://doi.org/10.1186/s13321-025-01082-5","pmid":"https://pubmed.ncbi.nlm.nih.gov/41131648"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-01082-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01082-5","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01082-5","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01082-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5093952428","display_name":"Adri\u00e1n Ro\u0161inec","orcid":"https://orcid.org/0000-0002-7748-5590"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":true,"raw_author_name":"Adri\u00e1n Ro\u0161inec","raw_affiliation_strings":["CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","Institute of Computer Science, Masaryk University, \u0160umavsk\u00e1 525/33, 602 00, Brno, Czech Republic","National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967"]},{"raw_affiliation_string":"Institute of Computer Science, Masaryk University, \u0160umavsk\u00e1 525/33, 602 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067283214","display_name":"Ter\u00e9zia Slanin\u00e1kov\u00e1","orcid":"https://orcid.org/0000-0003-0502-1145"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Ter\u00e9zia Slanin\u00e1kov\u00e1","raw_affiliation_strings":["Institute of Computer Science, Masaryk University, \u0160umavsk\u00e1 525/33, 602 00, Brno, Czech Republic. slaninakova@ics.muni.cz","National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic. slaninakova@ics.muni.cz","Institute of Computer Science, Masaryk University, \u0160umavsk\u00e1 525/33, 602 00, Brno, Czech Republic","National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Institute of Computer Science, Masaryk University, \u0160umavsk\u00e1 525/33, 602 00, Brno, Czech Republic. slaninakova@ics.muni.cz","institution_ids":["https://openalex.org/I21449261"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic. slaninakova@ics.muni.cz","institution_ids":["https://openalex.org/I21449261"]},{"raw_affiliation_string":"Institute of Computer Science, Masaryk University, \u0160umavsk\u00e1 525/33, 602 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037319451","display_name":"Tom\u00e1\u0161 Pavl\u00edk","orcid":"https://orcid.org/0000-0001-7166-032X"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Tom\u00e1\u0161 Pavl\u00edk","raw_affiliation_strings":["Institute of Computer Science, Masaryk University, \u0160umavsk\u00e1 525/33, 602 00, Brno, Czech Republic","National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Institute of Computer Science, Masaryk University, \u0160umavsk\u00e1 525/33, 602 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5120105218","display_name":"R\u00f3bert Randiak","orcid":null},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"R\u00f3bert Randiak","raw_affiliation_strings":["CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102997614","display_name":"Tom\u00e1\u0161 Svoboda","orcid":"https://orcid.org/0009-0006-3773-3082"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Tom\u00e1\u0161 Svoboda","raw_affiliation_strings":["CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","Institute of Computer Science, Masaryk University, \u0160umavsk\u00e1 525/33, 602 00, Brno, Czech Republic","National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967"]},{"raw_affiliation_string":"Institute of Computer Science, Masaryk University, \u0160umavsk\u00e1 525/33, 602 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040326443","display_name":"Tom\u00e1\u0161 Ra\u010dek","orcid":"https://orcid.org/0000-0002-0296-2452"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Tom\u00e1\u0161 Ra\u010dek","raw_affiliation_strings":["CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","Institute of Computer Science, Masaryk University, \u0160umavsk\u00e1 525/33, 602 00, Brno, Czech Republic","National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967"]},{"raw_affiliation_string":"Institute of Computer Science, Masaryk University, \u0160umavsk\u00e1 525/33, 602 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5099430632","display_name":"Gabriela Bu\u010dekov\u00e1","orcid":"https://orcid.org/0009-0000-3623-718X"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Gabriela Bu\u010dekov\u00e1","raw_affiliation_strings":["CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058084999","display_name":"Ond\u0159ej Schindler","orcid":"https://orcid.org/0000-0002-9047-0334"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Ond\u0159ej Schindler","raw_affiliation_strings":["CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034266620","display_name":"Matej Antol","orcid":"https://orcid.org/0000-0002-1380-5647"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Matej Antol","raw_affiliation_strings":["Institute of Computer Science, Masaryk University, \u0160umavsk\u00e1 525/33, 602 00, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Institute of Computer Science, Masaryk University, \u0160umavsk\u00e1 525/33, 602 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008958321","display_name":"Ale\u0161 K\u0159enek","orcid":"https://orcid.org/0000-0002-3395-3196"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Ale\u0161 K\u0159enek","raw_affiliation_strings":["Institute of Computer Science, Masaryk University, \u0160umavsk\u00e1 525/33, 602 00, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Institute of Computer Science, Masaryk University, \u0160umavsk\u00e1 525/33, 602 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049457524","display_name":"Karel Berka","orcid":"https://orcid.org/0000-0001-9472-2589"},"institutions":[{"id":"https://openalex.org/I70703428","display_name":"Palack\u00fd University Olomouc","ror":"https://ror.org/04qxnmv42","country_code":"CZ","type":"education","lineage":["https://openalex.org/I70703428"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Karel Berka","raw_affiliation_strings":["Department of Physical Chemistry, Faculty of Science, Palacky University, 17. listopadu 12, 779 00, Olomouc, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Department of Physical Chemistry, Faculty of Science, Palacky University, 17. listopadu 12, 779 00, Olomouc, Czech Republic","institution_ids":["https://openalex.org/I70703428"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051424845","display_name":"Radka Svobodov\u00e1 Va\u0159ekov\u00e1","orcid":"https://orcid.org/0000-0002-3840-8760"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Radka Svobodov\u00e1","raw_affiliation_strings":["CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic. radka.svobodova@ceitec.muni.cz","National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic. radka.svobodova@ceitec.muni.cz","National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic. radka.svobodova@ceitec.muni.cz","institution_ids":["https://openalex.org/I1310815967"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic. radka.svobodova@ceitec.muni.cz","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I21449261"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]},{"raw_affiliation_string":"CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":12,"corresponding_author_ids":["https://openalex.org/A5093952428"],"corresponding_institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I21449261"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.43592502,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"17","issue":"1","first_page":"160","last_page":"160"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11937","display_name":"Research Data Management Practices","score":0.9991000294685364,"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"}},"topics":[{"id":"https://openalex.org/T11937","display_name":"Research Data Management Practices","score":0.9991000294685364,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9983000159263611,"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/T11719","display_name":"Data Quality and Management","score":0.9779000282287598,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.8212000131607056},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5146999955177307},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.4636000096797943},{"id":"https://openalex.org/keywords/reuse","display_name":"Reuse","score":0.4027000069618225},{"id":"https://openalex.org/keywords/metadata-modeling","display_name":"Metadata modeling","score":0.3732999861240387},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.3294000029563904}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8539999723434448},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.8212000131607056},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5146999955177307},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4675999879837036},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.4636000096797943},{"id":"https://openalex.org/C206588197","wikidata":"https://www.wikidata.org/wiki/Q846574","display_name":"Reuse","level":2,"score":0.4027000069618225},{"id":"https://openalex.org/C110326360","wikidata":"https://www.wikidata.org/wiki/Q17149476","display_name":"Metadata modeling","level":4,"score":0.3732999861240387},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.34630000591278076},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.3294000029563904},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3050999939441681},{"id":"https://openalex.org/C76518257","wikidata":"https://www.wikidata.org/wiki/Q271680","display_name":"Software framework","level":5,"score":0.2962000072002411},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.2915000021457672},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.27570000290870667},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.2639999985694885},{"id":"https://openalex.org/C30872290","wikidata":"https://www.wikidata.org/wiki/Q1172389","display_name":"Data element","level":3,"score":0.2614000141620636},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.2587999999523163},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.25540000200271606}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-025-01082-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01082-5","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01082-5","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:41131648","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41131648","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":"Journal of cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:f0d65d888ada4fda8586072b08b76555","is_oa":true,"landing_page_url":"https://doaj.org/article/f0d65d888ada4fda8586072b08b76555","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":"Journal of Cheminformatics, Vol 17, Iss 1, Pp 1-10 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11356039","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12548288","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-025-01082-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01082-5","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01082-5","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4178066241","display_name":null,"funder_award_id":"LM2023055","funder_id":"https://openalex.org/F4320321005","funder_display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy"}],"funders":[{"id":"https://openalex.org/F4320321005","display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy","ror":"https://ror.org/037n8p820"},{"id":"https://openalex.org/F4320323870","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986"},{"id":"https://openalex.org/F4320326548","display_name":"Masarykova Univerzita","ror":"https://ror.org/02j46qs45"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4415462938.pdf","grobid_xml":"https://content.openalex.org/works/W4415462938.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W2081417077","https://openalex.org/W2170047619","https://openalex.org/W2302501749","https://openalex.org/W2807315575","https://openalex.org/W2889027537","https://openalex.org/W3188477560","https://openalex.org/W4294724553","https://openalex.org/W4309721430","https://openalex.org/W4388638767","https://openalex.org/W4388870515","https://openalex.org/W4393928012","https://openalex.org/W4400203469","https://openalex.org/W4404328867","https://openalex.org/W4404994414","https://openalex.org/W4407590534","https://openalex.org/W4409148148"],"related_works":[],"abstract_inverted_index":{"The":[0,70,98],"volume":[1],"of":[2,35,50,130,166,213,217],"molecular":[3,169],"dynamics":[4,170],"(MD)":[5,171],"simulation":[6,76,146,181],"data":[7,147],"shared":[8],"via":[9],"public":[10],"repositories":[11],"is":[12,100],"rapidly":[13],"increasing;":[14],"however,":[15],"fragmentation":[16],"across":[17],"multiple":[18],"independent":[19],"repositories,":[20],"each":[21],"employing":[22],"distinct":[23],"dataset":[24],"identifiers":[25],"and":[26,33,59,93,111,126,144,195,223],"metadata":[27,61,66,84,118,133,167,215],"schemas,":[28],"hinders":[29],"the":[30,63,73,80,83,117,128,149,163,211,228],"efficient":[31],"exploration":[32],"reuse":[34,145],"these":[36],"data.":[37],"In":[38],"this":[39],"study,":[40],"we":[41],"present":[42],"GROMACS":[43,54,65,121,135,157,176,208],"MetaDump,":[44,158],"a":[45,103,112,159,199,206],"tool":[46,71,99,161],"for":[47,82,162],"automatic":[48,164],"annotation":[49],"output":[51],"files":[52,95],"from":[53,91,134,168],"MD":[55,136,218],"simulations":[56,172],"producing":[57],"human-":[58],"machine-readable":[60],"leveraging":[62],"native":[64],"(gmx":[67],"dump)":[68],"output.":[69],"takes":[72],"run":[74],"input":[75],"file":[77],"(.tpr)":[78],"as":[79,102,184],"basis":[81],"output,":[85],"optionally":[86],"extending":[87],"it":[88,139],"with":[89,174,227],"annotations":[90,216],"topology":[92],"structure":[94],"(.top,":[96],".gro).":[97],"available":[101],"web":[104],"application":[105],"(":[106],"https://gmd.ceitec.cz/":[107],"),":[108],"API":[109],"service,":[110],"command-line":[113],"utility.":[114],"By":[115],"automating":[116],"extraction":[119,129,165],"process,":[120],"MetaDump":[122,177,209],"aims":[123],"to":[124,141],"simplify":[125],"standardise":[127],"rich,":[131],"structured":[132,200],"simulations,":[137,219],"making":[138,220],"easier":[140],"share,":[142],"discover,":[143],"within":[148],"research":[150],"community.":[151],"SCIENTIFIC":[152],"CONTRIBUTION:":[153],"This":[154],"work":[155],"introduces":[156],"software":[160,185],"performed":[173],"GROMACS.":[175],"captures":[178],"all":[179],"extractable":[180],"parameters,":[182],"such":[183],"version,":[186],"force":[187],"field,":[188],"water":[189],"model,":[190],"box":[191],"geometry,":[192],"temperature,":[193],"etc.,":[194],"returns":[196],"them":[197],"in":[198,225],"JSON":[201],"or":[202],"YAML":[203],"file.":[204],"As":[205],"result,":[207],"supports":[210],"creation":[212],"unified":[214],"datasets":[221],"indexable":[222],"findable":[224],"line":[226],"FAIR":[229],"principles.":[230]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-24T00:00:00"}
