{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T02:14:20Z","timestamp":1767838460581,"version":"3.49.0"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,2,11]],"date-time":"2020-02-11T00:00:00Z","timestamp":1581379200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Wellcome Trust PhD Studentship","award":["203756\/Z\/16\/A"],"award-info":[{"award-number":["203756\/Z\/16\/A"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>Structural biology relies on specific file formats to convey information about macromolecular structures. Traditionally this has been the PDB format, but increasingly newer formats, such as PDBML, mmCIF and MMTF are being used. Here we present atomium, a modern, lightweight, Python library for parsing, manipulating and saving PDB, mmCIF and MMTF file formats. In addition, we provide a web service, pdb2json, which uses atomium to give a consistent JSON representation to the entire Protein Data Bank.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>atomium is implemented in Python and its performance is equivalent to the existing library BioPython. However, it has significant advantages in features and API design. atomium is available from atomium.bioinf.org.uk and pdb2json can be accessed at pdb2json.bioinf.org.uk<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa072","type":"journal-article","created":{"date-parts":[[2020,2,3]],"date-time":"2020-02-03T20:10:35Z","timestamp":1580760635000},"page":"2750-2754","source":"Crossref","is-referenced-by-count":13,"title":["atomium\u2014a Python structure parser"],"prefix":"10.1093","volume":"36","author":[{"given":"Sam M","family":"Ireland","sequence":"first","affiliation":[{"name":"Division of Biosciences, Institute of Structural and Molecular Biology, University College London , London WC1E 6BT, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2835-2572","authenticated-orcid":false,"given":"Andrew C R","family":"Martin","sequence":"additional","affiliation":[{"name":"Division of Biosciences, Institute of Structural and Molecular Biology, University College London , London WC1E 6BT, UK"}]}],"member":"286","published-online":{"date-parts":[[2020,2,11]]},"reference":[{"key":"2023013110291587300_btaa072-B1","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1186\/s13321-016-0155-1","article-title":"Molmil: a molecular viewer for the PDB and beyond","volume":"8","author":"Bekker","year":"2016","journal-title":"J. Cheminformatics"},{"key":"2023013110291587300_btaa072-B2","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/S0022-2836(77)80200-3","article-title":"The Protein Data Bank: a computer-based archival file for macromolecular structures","volume":"112","author":"Bernstein","year":"1977","journal-title":"J. Mol. Biol"},{"key":"2023013110291587300_btaa072-B3","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1016\/S0076-6879(97)77032-0","volume-title":"Macromolecular Crystallography Part B, Vol. 277 of Methods in Enzymology","author":"Bourne","year":"1997"},{"key":"2023013110291587300_btaa072-B4","doi-asserted-by":"crossref","first-page":"e1005575","DOI":"10.1371\/journal.pcbi.1005575","article-title":"MMTF\u2014an efficient file format for the transmission, visualization, and analysis of macromolecular structures","volume":"13","author":"Bradley","year":"2017","journal-title":"PLoS Comput. 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