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Detecting pore-lining regions in transmembrane protein sequences.
Nugent T, Jones DT. Nugent T, et al. BMC Bioinformatics. 2012 Jul 17;13:169. doi: 10.1186/1471-2105-13-169. BMC Bioinformatics. 2012. PMID: 22805427 Free PMC article.
Scalable web services for the PSIPRED Protein Analysis Workbench.
Buchan DW, Minneci F, Nugent TC, Bryson K, Jones DT. Buchan DW, et al. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W349-57. doi: 10.1093/nar/gkt381. Epub 2013 Jun 8. Nucleic Acids Res. 2013. PMID: 23748958 Free PMC article.
FFPred: an integrated feature-based function prediction server for vertebrate proteomes.
Lobley AE, Nugent T, Orengo CA, Jones DT. Lobley AE, et al. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W297-302. doi: 10.1093/nar/gkn193. Epub 2008 May 7. Nucleic Acids Res. 2008. PMID: 18463141 Free PMC article.
De novo membrane protein structure prediction.
Nugent T. Nugent T. Methods Mol Biol. 2015;1215:331-50. doi: 10.1007/978-1-4939-1465-4_15. Methods Mol Biol. 2015. PMID: 25330970
Evaluation of predictions in the CASP10 model refinement category.
Nugent T, Cozzetto D, Jones DT. Nugent T, et al. Proteins. 2014 Feb;82 Suppl 2(Suppl 2):98-111. doi: 10.1002/prot.24377. Epub 2014 Jan 3. Proteins. 2014. PMID: 23900810 Free PMC article.
Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis.
Nugent T, Jones DT. Nugent T, et al. Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):E1540-7. doi: 10.1073/pnas.1120036109. Epub 2012 May 29. Proc Natl Acad Sci U S A. 2012. PMID: 22645369 Free PMC article.
Membrane protein structural bioinformatics.
Nugent T, Jones DT. Nugent T, et al. J Struct Biol. 2012 Sep;179(3):327-37. doi: 10.1016/j.jsb.2011.10.008. Epub 2011 Oct 31. J Struct Biol. 2012. PMID: 22075226 Review.
The MEMPACK alpha-helical transmembrane protein structure prediction server.
Nugent T, Ward S, Jones DT. Nugent T, et al. Bioinformatics. 2011 May 15;27(10):1438-9. doi: 10.1093/bioinformatics/btr096. Epub 2011 Feb 23. Bioinformatics. 2011. PMID: 21349872 Free PMC article.
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