{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T18:02:37Z","timestamp":1775325757959,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1576,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Secondary structure underpins the folding pattern and architecture of most proteins. Accurate assignment of the secondary structure elements is therefore an important problem. Although many approximate solutions of the secondary structure assignment problem exist, the statement of the problem has resisted a consistent and mathematically rigorous definition. A variety of comparative studies have highlighted major disagreements in the way the available methods define and assign secondary structure to coordinate data.<\/jats:p>\n               <jats:p>Results: We report a new method to infer secondary structure based on the Bayesian method of minimum message length inference. It treats assignments of secondary structure as hypotheses that explain the given coordinate data. The method seeks to maximize the joint probability of a hypothesis and the data. There is a natural null hypothesis and any assignment that cannot better it is unacceptable. We developed a program SST based on this approach and compared it with popular programs, such as DSSP and STRIDE among others. Our evaluation suggests that SST gives reliable assignments even on low-resolution structures.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/www.csse.monash.edu.au\/~karun\/sst<\/jats:p>\n               <jats:p>Contact: \u00a0arun.konagurthu@monash.edu (or lloyd.allison@monash.edu)<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts223","type":"journal-article","created":{"date-parts":[[2012,6,11]],"date-time":"2012-06-11T14:09:18Z","timestamp":1339423758000},"page":"i97-i105","source":"Crossref","is-referenced-by-count":39,"title":["Minimum message length inference of secondary structure from protein coordinate data"],"prefix":"10.1093","volume":"28","author":[{"given":"Arun S.","family":"Konagurthu","sequence":"first","affiliation":[{"name":"1 Clayton School of Information Technology, Monash University, Clayton VIC 3800, Australia and 2Department of Biochemistry and Molecular Biology and The Huck Institute for Genomics, Proteomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arthur M.","family":"Lesk","sequence":"additional","affiliation":[{"name":"1 Clayton School of Information Technology, Monash University, Clayton VIC 3800, Australia and 2Department of Biochemistry and Molecular Biology and The Huck Institute for Genomics, Proteomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lloyd","family":"Allison","sequence":"additional","affiliation":[{"name":"1 Clayton School of Information Technology, Monash University, Clayton VIC 3800, Australia and 2Department of Biochemistry and Molecular Biology and The Huck Institute for Genomics, Proteomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,6,9]]},"reference":[{"key":"2023012512392632500_B1","first-page":"459","article-title":"Secondary structure assignment","volume-title":"Structural Bioinformatics","author":"Andersen","year":"2009"},{"key":"2023012512392632500_B2","first-page":"370","article-title":"An essay towards solving a problem in the doctrine of chance","volume":"53","author":"Bayes","year":"1763","journal-title":"Philos. 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