{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:58:26Z","timestamp":1792789106568,"version":"4.5.0"},"reference-count":65,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2016,11,10]],"date-time":"2016-11-10T00:00:00Z","timestamp":1478736000000},"content-version":"vor","delay-in-days":73,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","award":["VR-NT 2012-5046"],"award-info":[{"award-number":["VR-NT 2012-5046"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The PRED-TMBB method is based on Hidden Markov Models and is capable of predicting the topology of beta-barrel outer membrane proteins and discriminate them from water-soluble ones. Here, we present an updated version of the method, PRED-TMBB2, with several newly developed features that improve its performance. The inclusion of a properly defined end state allows for better modeling of the beta-barrel domain, while different emission probabilities for the adjacent residues in strands are used to incorporate knowledge concerning the asymmetric amino acid distribution occurring there. Furthermore, the training was performed using newly developed algorithms in order to optimize the labels of the training sequences. Moreover, the method is retrained on a larger, non-redundant dataset which includes recently solved structures, and a newly developed decoding method was added to the already available options. Finally, the method now allows the incorporation of evolutionary information in the form of multiple sequence alignments.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>The results of a strict cross-validation procedure show that PRED-TMBB2 with homology information performs significantly better compared to other available prediction methods. It yields 76% in correct topology predictions and outperforms the best available predictor by 7%, with an overall SOV of 0.9. Regarding detection of beta-barrel proteins, PRED-TMBB2, using just the query sequence as input, achieves an MCC value of 0.92, outperforming even predictors designed for this task and are much slower.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>The method, along with all datasets used, is freely available for academic users at http:\/\/www.compgen.org\/tools\/PRED-TMBB2.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Contact<\/jats:title>\n                  <jats:p>pbagos@compgen.org<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw444","type":"journal-article","created":{"date-parts":[[2016,9,1]],"date-time":"2016-09-01T07:53:39Z","timestamp":1472716419000},"page":"i665-i671","source":"Crossref","is-referenced-by-count":88,"title":["PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins"],"prefix":"10.1093","volume":"32","author":[{"given":"Konstantinos D","family":"Tsirigos","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Biophysics, Science for Life Laboratory, Swedish E-Science Research Center, Stockholm University, 17121 Solna, Sweden"},{"name":"Department of Computer Science and Biomedical Informatics, University of Thessaly, 35100 Lamia, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arne","family":"Elofsson","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Biophysics, Science for Life Laboratory, Swedish E-Science Research Center, Stockholm University, 17121 Solna, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pantelis G","family":"Bagos","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Biomedical Informatics, University of Thessaly, 35100 Lamia, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,8,29]]},"reference":[{"key":"2023020113313478700_btw444-B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023020113313478700_btw444-B2","first-page":"40","volume-title":"ICGI 2004, LNAI","author":"Bagos","year":"2004"},{"key":"2023020113313478700_btw444-B3","doi-asserted-by":"crossref","first-page":"7.","DOI":"10.1186\/1471-2105-6-7","article-title":"Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method","volume":"6","author":"Bagos","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023020113313478700_btw444-B4","doi-asserted-by":"crossref","first-page":"189.","DOI":"10.1186\/1471-2105-7-189","article-title":"Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins","volume":"7","author":"Bagos","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023020113313478700_btw444-B5","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1186\/1471-2105-5-29","article-title":"A hidden Markov model method, capable of predicting and discriminating beta-barrel outer membrane proteins","volume":"5","author":"Bagos","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023020113313478700_btw444-B6","doi-asserted-by":"crossref","first-page":"W400","DOI":"10.1093\/nar\/gkh417","article-title":"PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins","volume":"32","author":"Bagos","year":"2004","journal-title":"Nucleic Acids Research"},{"key":"2023020113313478700_btw444-B7","doi-asserted-by":"crossref","first-page":"2811","DOI":"10.1093\/bioinformatics\/btq530","article-title":"Combined prediction of Tat and Sec signal peptides with hidden Markov models","volume":"26","author":"Bagos","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020113313478700_btw444-B8","doi-asserted-by":"crossref","first-page":"15370","DOI":"10.1073\/pnas.0808115105","article-title":"Structure of the human voltage-dependent anion channel","volume":"105","author":"Bayrhuber","year":"2008","journal-title":"Proc. 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