{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:41:38Z","timestamp":1772138498187,"version":"3.50.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,10,28]],"date-time":"2022-10-28T00:00:00Z","timestamp":1666915200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000038","name":"NSERC","doi-asserted-by":"publisher","award":["PG 22R3468"],"award-info":[{"award-number":["PG 22R3468"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005247","name":"UBC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005247","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Peter Wall Institute for Advanced Studies and Biotalent Canada"},{"DOI":"10.13039\/100000104","name":"National Aeronautics and Space Administration","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000104","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Recent advances in Cryo-EM led to a surge of ribosome structures deposited over the past years, including structures from different species, conformational states, or bound with different ligands. Yet, multiple conflicts of nomenclature make the identification and comparison of structures and ortholog components challenging. We present RiboXYZ (available at https:\/\/ribosome.xyz), a database that provides organized access to ribosome structures, with several tools for visualisation and study. The database is up-to-date with the Protein Data Bank (PDB) but provides a standardized nomenclature that allows for searching and comparing ribosomal components (proteins, RNA, ligands) across all the available structures. In addition to structured and simplified access to the data, the application has several specialized visualization tools, including the identification and prediction of ligand binding sites, and 3D superimposition of ribosomal components. Overall, RiboXYZ provides a useful toolkit that complements the PDB database, by implementing the current conventions and providing a set of auxiliary tools that have been developed explicitly for analyzing ribosome structures. This toolkit can be easily accessed by both experts and non-experts in structural biology so that they can search, visualize and compare structures, with various potential applications in molecular biology, evolution, and biochemistry.<\/jats:p>","DOI":"10.1093\/nar\/gkac939","type":"journal-article","created":{"date-parts":[[2022,10,12]],"date-time":"2022-10-12T17:25:53Z","timestamp":1665595553000},"page":"D509-D516","source":"Crossref","is-referenced-by-count":15,"title":["RiboXYZ: a comprehensive database for visualizing and analyzing ribosome structures"],"prefix":"10.1093","volume":"51","author":[{"given":"Artem","family":"Kushner","sequence":"first","affiliation":[{"name":"Department of Mathematics, University of British Columbia , Vancouver, BC V6T 1Z2, Canada"},{"name":"Department of Computer Science, University of British Columbia , Vancouver, BC V6T 1Z4, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3359-7299","authenticated-orcid":false,"given":"Anton S","family":"Petrov","sequence":"additional","affiliation":[{"name":"NASA Center for the Origin of Life, Georgia Institute of Technology , Atlanta, GA 30332-0400, USA"},{"name":"School of Biological Sciences, Georgia Institute of Technology , Atlanta, GA 30332, USA"},{"name":"School of Chemistry and Biochemistry, Georgia Institute of Technology , Atlanta, GA 30332, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9685-5171","authenticated-orcid":false,"given":"Khanh","family":"Dao\u00a0Duc","sequence":"additional","affiliation":[{"name":"Department of Mathematics, University of British Columbia , Vancouver, BC V6T 1Z2, Canada"},{"name":"Department of Computer Science, University of British Columbia , Vancouver, BC V6T 1Z4, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,10,28]]},"reference":[{"key":"2023010804200224200_B1","article-title":"Gene Machine: the race to decipher the secrets of the ribosome","volume-title":"Basic Books","author":"Ramakrishnan","year":"2018"},{"key":"2023010804200224200_B2","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/j.sbi.2017.06.002","article-title":"Cryo-EM: beyond the microscope","volume":"46","author":"Earl","year":"2017","journal-title":"Curr. 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