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OMPdb: a database of {beta}-barrel outer membrane proteins from Gram-negative bacteria.
Tsirigos KD, Bagos PG, Hamodrakas SJ. Tsirigos KD, et al. Nucleic Acids Res. 2011 Jan;39(Database issue):D324-31. doi: 10.1093/nar/gkq863. Epub 2010 Oct 15. Nucleic Acids Res. 2011. PMID: 20952406 Free PMC article.
JUCHMME: a Java Utility for Class Hidden Markov Models and Extensions for biological sequence analysis.
Tamposis IA, Tsirigos KD, Theodoropoulou MC, Kontou PI, Tsaousis GN, Sarantopoulou D, Litou ZI, Bagos PG. Tamposis IA, et al. Among authors: tsirigos kd. Bioinformatics. 2019 Dec 15;35(24):5309-5312. doi: 10.1093/bioinformatics/btz533. Bioinformatics. 2019. PMID: 31250907
PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins.
Tsirigos KD, Elofsson A, Bagos PG. Tsirigos KD, et al. Bioinformatics. 2016 Sep 1;32(17):i665-i671. doi: 10.1093/bioinformatics/btw444. Bioinformatics. 2016. PMID: 27587687
Combined prediction of Tat and Sec signal peptides with hidden Markov models.
Bagos PG, Nikolaou EP, Liakopoulos TD, Tsirigos KD. Bagos PG, et al. Among authors: tsirigos kd. Bioinformatics. 2010 Nov 15;26(22):2811-7. doi: 10.1093/bioinformatics/btq530. Epub 2010 Sep 16. Bioinformatics. 2010. PMID: 20847219
ExTopoDB: a database of experimentally derived topological models of transmembrane proteins.
Tsaousis GN, Tsirigos KD, Andrianou XD, Liakopoulos TD, Bagos PG, Hamodrakas SJ. Tsaousis GN, et al. Among authors: tsirigos kd. Bioinformatics. 2010 Oct 1;26(19):2490-2. doi: 10.1093/bioinformatics/btq362. Epub 2010 Jul 3. Bioinformatics. 2010. PMID: 20601677
Prediction of cell wall sorting signals in gram-positive bacteria with a hidden markov model: application to complete genomes.
Litou ZI, Bagos PG, Tsirigos KD, Liakopoulos TD, Hamodrakas SJ. Litou ZI, et al. Among authors: tsirigos kd. J Bioinform Comput Biol. 2008 Apr;6(2):387-401. doi: 10.1142/s0219720008003382. J Bioinform Comput Biol. 2008. PMID: 18464329
Prediction of lipoprotein signal peptides in Gram-positive bacteria with a Hidden Markov Model.
Bagos PG, Tsirigos KD, Liakopoulos TD, Hamodrakas SJ. Bagos PG, et al. Among authors: tsirigos kd. J Proteome Res. 2008 Dec;7(12):5082-93. doi: 10.1021/pr800162c. J Proteome Res. 2008. PMID: 19367716
DisProt 7.0: a major update of the database of disordered proteins.
Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, Minervini G, Murvai N, Pujols J, Roche DB, Salladini E, Schad E, Schramm A, Szabo B, Tantos A, Tonello F, Tsirigos KD, Veljković N, Ventura S, Vranken W, Warholm P, Uversky VN, Dunker AK, Longhi S, Tompa P, Tosatto SC. Piovesan D, et al. Among authors: tsirigos kd. Nucleic Acids Res. 2017 Jan 4;45(D1):D219-D227. doi: 10.1093/nar/gkw1056. Epub 2016 Nov 28. Nucleic Acids Res. 2017. PMID: 27899601 Free PMC article.
Corrigendum: DisProt 7.0: a major update of the database of disordered proteins.
Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, Minervini G, Murvai N, Pujols J, Roche DB, Salladini E, Schad E, Schramm A, Szabo B, Tantos A, Tonello F, Tsirigos KD, Veljković N, Ventura S, Vranken W, Warholm P, Uversky VN, Dunker AK, Longhi S, Tompa P, Tosatto SC. Piovesan D, et al. Among authors: tsirigos kd. Nucleic Acids Res. 2017 Jan 4;45(D1):D1123-D1124. doi: 10.1093/nar/gkw1279. Epub 2016 Dec 13. Nucleic Acids Res. 2017. PMID: 27965415 Free PMC article. No abstract available.
Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.
Babbitt PC, Bagos PG, Bairoch A, Bateman A, Chatonnet A, Chen MJ, Craik DJ, Finn RD, Gloriam D, Haft DH, Henrissat B, Holliday GL, Isberg V, Kaas Q, Landsman D, Lenfant N, Manning G, Nagano N, Srinivasan N, O'Donovan C, Pruitt KD, Sowdhamini R, Rawlings ND, Saier MH Jr, Sharman JL, Spedding M, Tsirigos KD, Vastermark A, Vriend G. Babbitt PC, et al. Among authors: tsirigos kd. Database (Oxford). 2015 Jul 11;2015:bav063. doi: 10.1093/database/bav063. eCollection 2015. Database (Oxford). 2015. PMID: 26284514 Free PMC article.
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