{"id":"https://openalex.org/W3211774640","doi":"https://doi.org/10.1093/bioinformatics/btab785","title":"Biobox: a toolbox for biomolecular modelling","display_name":"Biobox: a toolbox for biomolecular modelling","publication_year":2021,"publication_date":"2021-11-11","ids":{"openalex":"https://openalex.org/W3211774640","doi":"https://doi.org/10.1093/bioinformatics/btab785","mag":"3211774640","pmid":"https://pubmed.ncbi.nlm.nih.gov/34791029"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab785","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab785","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/4/1149/42319911/btab785.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/4/1149/42319911/btab785.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046455203","display_name":"Lucas S. P. Rudden","orcid":"https://orcid.org/0000-0002-4753-8890"},"institutions":[{"id":"https://openalex.org/I190082696","display_name":"Durham University","ror":"https://ror.org/01v29qb04","country_code":"GB","type":"education","lineage":["https://openalex.org/I190082696"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Lucas S P Rudden","raw_affiliation_strings":["Department of Physics, Durham University , DurhamDH1 3LE, UK"],"raw_orcid":"https://orcid.org/0000-0002-4753-8890","affiliations":[{"raw_affiliation_string":"Department of Physics, Durham University , DurhamDH1 3LE, UK","institution_ids":["https://openalex.org/I190082696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000252047","display_name":"Samuel C. Musson","orcid":"https://orcid.org/0000-0002-2189-554X"},"institutions":[{"id":"https://openalex.org/I190082696","display_name":"Durham University","ror":"https://ror.org/01v29qb04","country_code":"GB","type":"education","lineage":["https://openalex.org/I190082696"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Samuel C Musson","raw_affiliation_strings":["Department of Physics, Durham University , DurhamDH1 3LE, UK"],"raw_orcid":"https://orcid.org/0000-0002-2189-554X","affiliations":[{"raw_affiliation_string":"Department of Physics, Durham University , DurhamDH1 3LE, UK","institution_ids":["https://openalex.org/I190082696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087357794","display_name":"Justin L. P. Benesch","orcid":"https://orcid.org/0000-0002-1507-3742"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Justin L P Benesch","raw_affiliation_strings":["Department of Chemistry, Biochemistry Building, University of Oxford , Oxford OX1 3QU, UK"],"raw_orcid":"https://orcid.org/0000-0002-1507-3742","affiliations":[{"raw_affiliation_string":"Department of Chemistry, Biochemistry Building, University of Oxford , Oxford OX1 3QU, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071713921","display_name":"Matteo T. Degiacomi","orcid":"https://orcid.org/0000-0003-4672-471X"},"institutions":[{"id":"https://openalex.org/I190082696","display_name":"Durham University","ror":"https://ror.org/01v29qb04","country_code":"GB","type":"education","lineage":["https://openalex.org/I190082696"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Matteo T Degiacomi","raw_affiliation_strings":["Department of Physics, Durham University , DurhamDH1 3LE, UK"],"raw_orcid":"https://orcid.org/0000-0003-4672-471X","affiliations":[{"raw_affiliation_string":"Department of Physics, Durham University , DurhamDH1 3LE, UK","institution_ids":["https://openalex.org/I190082696"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5071713921"],"corresponding_institution_ids":["https://openalex.org/I190082696"],"apc_list":{"value":3478,"currency":"USD","value_usd":3478},"apc_paid":{"value":3478,"currency":"USD","value_usd":3478},"fwci":0.2238,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.50024773,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"38","issue":"4","first_page":"1149","last_page":"1151"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9994000196456909,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9994000196456909,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9986000061035156,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9929999709129333,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.9463649988174438},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.9056299924850464},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8015271425247192},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.65205317735672},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.5378486514091492},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.34903767704963684},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3252485990524292}],"concepts":[{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.9463649988174438},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.9056299924850464},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8015271425247192},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.65205317735672},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.5378486514091492},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.34903767704963684},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3252485990524292}],"mesh":[{"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1093/bioinformatics/btab785","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab785","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/4/1149/42319911/btab785.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34791029","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34791029","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":"Journal Article"},{"id":"pmh:oai:dro.dur.ac.uk.OAI2:34653","is_oa":true,"landing_page_url":"http://dro.dur.ac.uk/34653/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400188","display_name":"Durham Research Online (Durham University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I190082696","host_organization_name":"Durham University","host_organization_lineage":["https://openalex.org/I190082696"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Bioinformatics, 2022, Vol.38(4), pp.1149-1151 [Peer Reviewed Journal]","raw_type":"Article"},{"id":"pmh:oai:ora.ox.ac.uk:uuid:b1f499c8-6291-421c-ad0a-b7a7380ae150","is_oa":true,"landing_page_url":"https://ora.ox.ac.uk/objects/uuid:b1f499c8-6291-421c-ad0a-b7a7380ae150","pdf_url":"https://ora.ox.ac.uk/objects/uuid:b1f499c8-6291-421c-ad0a-b7a7380ae150","source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"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":"Symplectic Elements","raw_type":"Journal article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8796382","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8796382","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:durham-repository.worktribe.com:1222790","is_oa":true,"landing_page_url":"https://durham-repository.worktribe.com/output/1222790","pdf_url":null,"source":{"id":"https://openalex.org/S4306400188","display_name":"Durham Research Online (Durham University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I190082696","host_organization_name":"Durham University","host_organization_lineage":["https://openalex.org/I190082696"],"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":"Journal Article"},{"id":"pmh:oai:pure.ed.ac.uk:openaire/179070e2-2f44-491f-831b-f7aabd74fb21","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/179070e2-2f44-491f-831b-f7aabd74fb21","pdf_url":null,"source":{"id":"https://openalex.org/S4306400321","display_name":"Edinburgh Research Explorer (University of Edinburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98677209","host_organization_name":"University of Edinburgh","host_organization_lineage":["https://openalex.org/I98677209"],"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":"Rudden, L S P, Musson, S C, Benesch, J L P & Degiacomi, M T 2021, 'Biobox : A toolbox for biomolecular modelling', Bioinformatics, vol. 38, no. 4, pp. 1149-1151. https://doi.org/10.1093/bioinformatics/btab785","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab785","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab785","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/4/1149/42319911/btab785.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4150660459","display_name":null,"funder_award_id":"EP/P016499/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G6027544220","display_name":"Software for experimentally driven macromolecular modelling","funder_award_id":"EP/P016499/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320320290","display_name":"University of Oxford","ror":"https://ror.org/052gg0110"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3211774640.pdf","grobid_xml":"https://content.openalex.org/works/W3211774640.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1978496023","https://openalex.org/W1991832340","https://openalex.org/W2011741494","https://openalex.org/W2102129683","https://openalex.org/W2146292423","https://openalex.org/W2158528359","https://openalex.org/W2170711116","https://openalex.org/W2179022142","https://openalex.org/W2569105298","https://openalex.org/W2707646777","https://openalex.org/W2760627581","https://openalex.org/W2799660409","https://openalex.org/W2883667768","https://openalex.org/W2965050052","https://openalex.org/W3035965352","https://openalex.org/W3099878876","https://openalex.org/W3110608029","https://openalex.org/W3131435592"],"related_works":["https://openalex.org/W2549786917","https://openalex.org/W235620669","https://openalex.org/W2964721899","https://openalex.org/W2123495936","https://openalex.org/W2324336873","https://openalex.org/W2797837731","https://openalex.org/W4210570868","https://openalex.org/W2996080391","https://openalex.org/W4381516792","https://openalex.org/W4226137555"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1],"implementation":[2,38],"of":[3,25,39],"biomolecular":[4,40],"modelling":[5,41],"methods":[6],"and":[7,21,56],"analyses":[8],"can":[9],"be":[10],"cumbersome,":[11],"often":[12],"carried":[13],"out":[14],"with":[15,53],"in-house":[16],"software":[17,27],"reimplementing":[18],"common":[19],"tasks,":[20],"requiring":[22],"the":[23,37],"integration":[24],"diverse":[26],"libraries.":[28],"RESULTS:":[29],"We":[30],"present":[31],"Biobox,":[32],"a":[33],"Python-based":[34],"toolbox":[35],"facilitating":[36],"methods.":[42],"AVAILABILITY":[43],"AND":[44],"IMPLEMENTATION:":[45],"Biobox":[46],"is":[47],"freely":[48],"available":[49],"on":[50],"https://github.com/degiacom/biobox,":[51],"along":[52],"its":[54],"API":[55],"interactive":[57],"Jupyter":[58],"notebook":[59],"tutorials.":[60]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2}],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2025-10-10T00:00:00"}
