{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T00:17:44Z","timestamp":1780877864691,"version":"3.54.1"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2021,11,15]],"date-time":"2021-11-15T00:00:00Z","timestamp":1636934400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council fellowship","doi-asserted-by":"crossref","award":["EP\/P016499\/1"],"award-info":[{"award-number":["EP\/P016499\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Impact Accelerator funds from the Engineering and Physical Sciences Research Council","award":["EP\/K503769\/1"],"award-info":[{"award-number":["EP\/K503769\/1"]}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000769","name":"University of Oxford","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100000769","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The implementation of biomolecular modelling methods and analyses can be cumbersome, often carried out with in-house software reimplementing common tasks, and requiring the integration of diverse software libraries.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present Biobox, a Python-based toolbox facilitating the implementation of biomolecular modelling methods.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Biobox is freely available on https:\/\/github.com\/degiacom\/biobox, along with its API and interactive Jupyter notebook tutorials.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab785","type":"journal-article","created":{"date-parts":[[2021,11,11]],"date-time":"2021-11-11T20:14:12Z","timestamp":1636661652000},"page":"1149-1151","source":"Crossref","is-referenced-by-count":7,"title":["Biobox: a toolbox for biomolecular modelling"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4753-8890","authenticated-orcid":false,"given":"Lucas S P","family":"Rudden","sequence":"first","affiliation":[{"name":"Department of Physics, Durham University , DurhamDH1 3LE, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2189-554X","authenticated-orcid":false,"given":"Samuel C","family":"Musson","sequence":"additional","affiliation":[{"name":"Department of Physics, Durham University , DurhamDH1 3LE, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1507-3742","authenticated-orcid":false,"given":"Justin L P","family":"Benesch","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Biochemistry Building, University of Oxford , Oxford OX1 3QU, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4672-471X","authenticated-orcid":false,"given":"Matteo T","family":"Degiacomi","sequence":"additional","affiliation":[{"name":"Department of Physics, Durham University , DurhamDH1 3LE, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,11,15]]},"reference":[{"key":"2023020108535584600_btab785-B1","doi-asserted-by":"crossref","first-page":"1855","DOI":"10.1016\/j.str.2011.09.015","article-title":"The polydispersity of \u03b1b-crystallin is rationalized by an interconverting polyhedral architecture","volume":"19","author":"Baldwin","year":"2011","journal-title":"Structure"},{"key":"2023020108535584600_btab785-B2","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1007\/s13361-018-1974-2","article-title":"On the effect of sphere-overlap on super coarse-grained models of protein assemblies","volume":"30","author":"Degiacomi","year":"2019","journal-title":"J. Am. Soc. Mass Spectrom"},{"key":"2023020108535584600_btab785-B3","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1039\/C5AN01636C","article-title":"EM\u2229IM: software for relating ion mobility mass spectrometry and electron microscopy data","volume":"141","author":"Degiacomi","year":"2016","journal-title":"Analyst"},{"key":"2023020108535584600_btab785-B4","doi-asserted-by":"crossref","first-page":"1751","DOI":"10.1016\/j.str.2017.08.015","article-title":"Accommodating protein dynamics in the modeling of chemical crosslinks","volume":"25","author":"Degiacomi","year":"2017","journal-title":"Structure"},{"key":"2023020108535584600_btab785-B5","doi-asserted-by":"crossref","first-page":"1212","DOI":"10.1107\/S1600576717007786","article-title":"Atsas 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions","volume":"50","author":"Franke","year":"2017","journal-title":"J. Appl. Crystallogr"},{"key":"2023020108535584600_btab785-B6","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/s41586-020-2649-2","article-title":"Array programming with numpy","volume":"585","author":"Harris","year":"2020","journal-title":"Nature"},{"key":"2023020108535584600_btab785-B7","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1002\/(SICI)1096-987X(20000130)21:2<79::AID-JCC1>3.0.CO;2-B","article-title":"The molecular modeling toolkit: a new approach to molecular simulations","volume":"21","author":"Hinsen","year":"2000","journal-title":"J. Comput. Chem"},{"key":"2023020108535584600_btab785-B8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/ncomms13993","article-title":"Integrating mass spectrometry with MD simulations reveals the role of lipids in Na+\/H+ antiporters","volume":"8","author":"Landreh","year":"2017","journal-title":"Nat. Commun"},{"key":"2023020108535584600_btab785-B9","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1016\/j.str.2015.02.010","article-title":"Collision cross sections for structural proteomics","volume":"23","author":"Marklund","year":"2015","journal-title":"Structure"},{"key":"2023020108535584600_btab785-B10","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1111\/mmi.13267","article-title":"Characterisation of Shigella Spa33 and Thermotoga FliM\/N reveals a new model for C-ring assembly in T3SS","volume":"99","author":"Mcdowell","year":"2016","journal-title":"Mol. Microbiol"},{"key":"2023020108535584600_btab785-B11","first-page":"56","volume-title":"Proceedings of the 9th Python in Science Conference, Austin, Texas","author":"McKinney","year":"2010"},{"key":"2023020108535584600_btab785-B12","doi-asserted-by":"crossref","first-page":"2319","DOI":"10.1002\/jcc.21787","article-title":"MDAnalysis: a toolkit for the analysis of molecular dynamics simulations","volume":"32","author":"Michaud-Agrawal","year":"2011","journal-title":"J. Comput. Chem"},{"key":"2023020108535584600_btab785-B13","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1016\/j.chempr.2020.11.011","article-title":"Mass photometry of membrane proteins","volume":"7","author":"Olerinyova","year":"2021","journal-title":"Chem"},{"key":"2023020108535584600_btab785-B14","doi-asserted-by":"crossref","first-page":"5135","DOI":"10.1021\/acs.jctc.9b00474","article-title":"Protein docking using a single representation for protein surface, electrostatics, and local dynamics","volume":"15","author":"Rudden","year":"2019","journal-title":"J. Chem. Theory Comput"},{"key":"2023020108535584600_btab785-B15","doi-asserted-by":"crossref","first-page":"1493","DOI":"10.1021\/acs.jcim.0c01315","article-title":"Transmembrane protein docking with jabberdock","volume":"61","author":"Rudden","year":"2021","journal-title":"J. Chem. Inform. Model"},{"key":"2023020108535584600_btab785-B16","doi-asserted-by":"crossref","first-page":"e1001244","DOI":"10.1371\/journal.pbio.1001244","article-title":"Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies","volume":"10","author":"Russel","year":"2012","journal-title":"PLoS Biol"},{"key":"2023020108535584600_btab785-B17","doi-asserted-by":"crossref","first-page":"19511","DOI":"10.1074\/jbc.RA118.005421","article-title":"It takes a dimer to tango: oligomeric small heat shock proteins dissociate to capture substrate","volume":"293","author":"Santhanagopalan","year":"2018","journal-title":"J. Biol. Chem"},{"key":"2023020108535584600_btab785-B18","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1109\/MCSE.2011.37","article-title":"The numpy array: a structure for efficient numerical computation","volume":"13","author":"van der Walt","year":"2011","journal-title":"Comput. Sci. Eng"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab785\/41512288\/btab785.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/4\/1149\/49009137\/btab785.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/4\/1149\/49009137\/btab785.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T20:15:23Z","timestamp":1675282523000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/4\/1149\/6428530"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2021,11,15]]},"references-count":18,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2022,1,27]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab785","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,2,15]]},"published":{"date-parts":[[2021,11,15]]}}}