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Items: 1 to 20 of 85

1.

Improving the detection of transmembrane β-barrel chains with N-to-1 extreme learning machines.

Savojardo C, Fariselli P, Casadio R.

Bioinformatics. 2011 Nov 15;27(22):3123-8. doi: 10.1093/bioinformatics/btr549.

PMID:
21967762
2.

BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes.

Savojardo C, Fariselli P, Casadio R.

Bioinformatics. 2013 Feb 15;29(4):504-5. doi: 10.1093/bioinformatics/bts728.

PMID:
23297037
3.
4.
5.

transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels.

Waldispühl J, Berger B, Clote P, Steyaert JM.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W189-93.

6.

PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins.

Bagos PG, Liakopoulos TD, Spyropoulos IC, Hamodrakas SJ.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W400-4.

7.

A highly accurate statistical approach for the prediction of transmembrane beta-barrels.

Freeman TC Jr, Wimley WC.

Bioinformatics. 2010 Aug 15;26(16):1965-74. doi: 10.1093/bioinformatics/btq308.

8.

Predicting transmembrane beta-barrels and interstrand residue interactions from sequence.

Waldispühl J, Berger B, Clote P, Steyaert JM.

Proteins. 2006 Oct 1;65(1):61-74.

PMID:
16858668
9.

TMBB-DB: a transmembrane β-barrel proteome database.

Freeman TC Jr, Wimley WC.

Bioinformatics. 2012 Oct 1;28(19):2425-30.

10.

Charge asymmetry in the proteins of the outer membrane.

Slusky JS, Dunbrack RL Jr.

Bioinformatics. 2013 Sep 1;29(17):2122-8. doi: 10.1093/bioinformatics/btt355.

11.

Biogenesis of beta-barrel proteins in evolutionary context.

Ulrich T, Rapaport D.

Int J Med Microbiol. 2015 Feb;305(2):259-64. doi: 10.1016/j.ijmm.2014.12.009. Review.

PMID:
25596888
12.

TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins.

Randall A, Cheng J, Sweredoski M, Baldi P.

Bioinformatics. 2008 Feb 15;24(4):513-20.

PMID:
18006547
13.
14.

Biogenesis of beta-barrel membrane proteins in bacteria and eukaryotes: evolutionary conservation and divergence.

Walther DM, Rapaport D, Tommassen J.

Cell Mol Life Sci. 2009 Sep;66(17):2789-804. doi: 10.1007/s00018-009-0029-z. Review.

15.

BOCTOPUS: improved topology prediction of transmembrane β barrel proteins.

Hayat S, Elofsson A.

Bioinformatics. 2012 Feb 15;28(4):516-22. doi: 10.1093/bioinformatics/btr710.

PMID:
22247276
16.

BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria.

Berven FS, Flikka K, Jensen HB, Eidhammer I.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W394-9.

17.

Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins.

Gromiha MM, Ahmad S, Suwa M.

J Comput Chem. 2004 Apr 15;25(5):762-7.

PMID:
14978719
18.

beta-Barrel transmembrane proteins: Geometric modelling, detection of transmembrane region, and structural properties.

Valavanis IK, Bagos PG, Emiris IZ.

Comput Biol Chem. 2006 Dec;30(6):416-24.

PMID:
17097352
19.

The structural biology of β-barrel membrane proteins: a summary of recent reports.

Fairman JW, Noinaj N, Buchanan SK.

Curr Opin Struct Biol. 2011 Aug;21(4):523-31. doi: 10.1016/j.sbi.2011.05.005. Review.

20.

Protein secondary structure prediction with SPARROW.

Bettella F, Rasinski D, Knapp EW.

J Chem Inf Model. 2012 Feb 27;52(2):545-56. doi: 10.1021/ci200321u.

PMID:
22224407
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