{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,30]],"date-time":"2025-04-30T11:28:03Z","timestamp":1746012483640},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1485,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,11,1]]},"abstract":"Abstract<\/jats:title>\n Pythoscape is a framework implemented in Python for processing large protein similarity networks for visualization in other software packages. Protein similarity networks are graphical representations of sequence, structural and other similarities among proteins for which pairwise all-by-all similarity connections have been calculated. Mapping of biological and other information to network nodes or edges enables hypothesis creation about sequence\u2013structure\u2013function relationships across sets of related proteins. Pythoscape provides several options to calculate pairwise similarities for input sequences or structures, applies filters to network edges and defines sets of similar nodes and their associated data as single nodes (termed representative nodes) for compression of network information and output data or formatted files for visualization.<\/jats:p>\n Contact: \u00a0babbitt@cgl.ucsf.edu<\/jats:p>\n Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts532","type":"journal-article","created":{"date-parts":[[2012,9,9]],"date-time":"2012-09-09T00:29:08Z","timestamp":1347150548000},"page":"2845-2846","source":"Crossref","is-referenced-by-count":42,"title":["Pythoscape: a framework for generation of large protein similarity networks"],"prefix":"10.1093","volume":"28","author":[{"suffix":"II","given":"Alan E.","family":"Barber","sequence":"first","affiliation":[{"name":"Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA"}]},{"given":"Patricia C.","family":"Babbitt","sequence":"additional","affiliation":[{"name":"Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA"}]}],"member":"286","published-online":{"date-parts":[[2012,9,8]]},"reference":[{"key":"2023012513152630900_bts532-B1","doi-asserted-by":"crossref","first-page":"11108","DOI":"10.1021\/bi901180v","article-title":"Glutathione transferases are structural and functional outliers in the thioredoxin fold","volume":"48","author":"Atkinson","year":"2009","journal-title":"Biochemistry"},{"key":"2023012513152630900_bts532-B2","doi-asserted-by":"crossref","first-page":"e4345","DOI":"10.1371\/journal.pone.0004345","article-title":"Using sequence similarity networks for visualization of relationships across diverse protein superfamilies","volume":"4","author":"Atkinson","year":"2009","journal-title":"PLoS One"},{"key":"2023012513152630900_bts532-B3","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1074\/jbc.R111.283408","article-title":"Inference of functional properties from large-scale analysis of enzyme superfamilies","volume":"287","author":"Brown","year":"2012","journal-title":"J. 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