{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:50Z","timestamp":1772138090886,"version":"3.50.1"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2018,11,16]],"date-time":"2018-11-16T00:00:00Z","timestamp":1542326400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004326","name":"Bayer AG","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004326","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Single-guide RNAs (sgRNAs) targeting the same gene can significantly vary in terms of efficacy and specificity. PAVOOC (Prediction And Visualization of On- and Off-targets for CRISPR) is a web-based CRISPR sgRNA design tool that employs state of the art machine learning models to prioritize most effective candidate sgRNAs. In contrast to other tools, it maps sgRNAs to functional domains and protein structures and visualizes cut sites on corresponding protein crystal structures. Furthermore, PAVOOC supports homology-directed repair template generation for genome editing experiments and the visualization of the mutated amino acids in 3D.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>PAVOOC is available under https:\/\/pavooc.me and accessible using modern browsers (Chrome\/Chromium recommended). The source code is hosted at github.com\/moritzschaefer\/pavooc under the MIT License. The backend, including data processing steps, and the frontend are implemented in Python 3 and ReactJS, respectively. All components run in a simple Docker environment.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty935","type":"journal-article","created":{"date-parts":[[2018,11,15]],"date-time":"2018-11-15T16:50:13Z","timestamp":1542300613000},"page":"2309-2310","source":"Crossref","is-referenced-by-count":10,"title":["PAVOOC: designing CRISPR sgRNAs using 3D protein structures and functional domain annotations"],"prefix":"10.1093","volume":"35","author":[{"given":"Moritz","family":"Schaefer","sequence":"first","affiliation":[{"name":"Computer Science, TU Berlin, D-10623 Berlin, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Djork-Arn\u00e9","family":"Clevert","sequence":"additional","affiliation":[{"name":"Bioinformatics, Bayer AG, D-13342 Berlin, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bertram","family":"Weiss","sequence":"additional","affiliation":[{"name":"Bioinformatics, Bayer AG, D-13342 Berlin, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Steffen","sequence":"additional","affiliation":[{"name":"Bioinformatics, Bayer AG, D-13342 Berlin, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,11,16]]},"reference":[{"key":"2023051612105790600_bty935-B1","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/nature11003","article-title":"The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity","volume":"483","author":"Barretina","year":"2012","journal-title":"Nature"},{"key":"2023051612105790600_bty935-B2","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2023051612105790600_bty935-B3","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1126\/science.1231143","article-title":"Multiplex genome engineering using CRISPR\/Cas systems","volume":"339","author":"Cong","year":"2013","journal-title":"Science"},{"key":"2023051612105790600_bty935-B4","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/35057062","article-title":"Initial sequencing and analysis of the human genome","volume":"409","author":"Consortium","year":"2001","journal-title":"Nature"},{"key":"2023051612105790600_bty935-B5","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1038\/nbt.3437","article-title":"Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9","volume":"34","author":"Doench","year":"2016","journal-title":"Nat. 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