{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,10,10]],"date-time":"2023-10-10T02:46:38Z","timestamp":1696905998389},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2707,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Amino acid residues are under various kinds of local environmental restraints, which influence substitution patterns. Ulla,1 a program for calculating environment-specific substitution tables, reads protein sequence alignments and local environment annotations. The program produces a substitution table for every possible combination of environment features. Sparse data is handled using an entropy-based smoothing procedure to estimate robust substitution probabilities.<\/jats:p>\n               <jats:p>Availability: The Ruby source code is available under a Creative Commons Attribution-Noncommercial License along with additional documentation from http:\/\/www-cryst.bioc.cam.ac.uk\/ulla.<\/jats:p>\n               <jats:p>Contact: \u00a0semin@cryst.bioc.cam.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp300","type":"journal-article","created":{"date-parts":[[2009,5,6]],"date-time":"2009-05-06T02:34:31Z","timestamp":1241577271000},"page":"1976-1977","source":"Crossref","is-referenced-by-count":11,"title":["Ulla: a program for calculating environment-specific amino acid substitution tables"],"prefix":"10.1093","volume":"25","author":[{"given":"Semin","family":"Lee","sequence":"first","affiliation":[{"name":"Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Old Addenbrooke's Site, Cambridge CB2 1GA, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tom L.","family":"Blundell","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Old Addenbrooke's Site, Cambridge CB2 1GA, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,5,5]]},"reference":[{"key":"2023013112092286500_B1","doi-asserted-by":"crossref","first-page":"1487","DOI":"10.1016\/j.jmb.2004.08.022","article-title":"Distinguishing structural and functional restraints in evolution in order to identify interaction sites","volume":"342","author":"Chelliah","year":"2004","journal-title":"J. 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An approach to the knowledge-based prediction of local structures in globular proteins","volume":"213","author":"Sippl","year":"1990","journal-title":"J. Mol. Biol."},{"key":"2023013112092286500_B10","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1006\/jmbi.1993.1018","article-title":"Fragment ranking in modelling of protein structure. Conformationally constrained environmental amino acid substitution tables","volume":"229","author":"Topham","year":"1993","journal-title":"J. Mol. 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