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Items: 16

1.

Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase.

Venko K, Roy Choudhury A, Novič M.

Comput Struct Biotechnol J. 2017 Jan 31;15:232-242. doi: 10.1016/j.csbj.2017.01.008. eCollection 2017. Review.

2.

OMPcontact: An Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method.

Zhang L, Wang H, Yan L, Su L, Xu D.

J Comput Biol. 2017 Mar;24(3):217-228. doi: 10.1089/cmb.2015.0236. Epub 2016 Aug 11.

PMID:
27513917
3.

All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences.

Hayat S, Sander C, Marks DS, Elofsson A.

Proc Natl Acad Sci U S A. 2015 Apr 28;112(17):5413-8. doi: 10.1073/pnas.1419956112. Epub 2015 Apr 9.

4.

Structural plasticity in the topology of the membrane-interacting domain of HIV-1 gp41.

Kyrychenko A, Freites JA, He J, Tobias DJ, Wimley WC, Ladokhin AS.

Biophys J. 2014 Feb 4;106(3):610-20. doi: 10.1016/j.bpj.2013.12.032.

5.
6.

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

Freeman TC Jr, Wimley WC.

Bioinformatics. 2012 Oct 1;28(19):2425-30. Epub 2012 Jul 27.

7.

Ranking models of transmembrane β-barrel proteins using Z-coordinate predictions.

Hayat S, Elofsson A.

Bioinformatics. 2012 Jun 15;28(12):i90-6. doi: 10.1093/bioinformatics/bts233.

8.

Predicting the outer membrane proteome of Pasteurella multocida based on consensus prediction enhanced by results integration and manual confirmation.

E-komon T, Burchmore R, Herzyk P, Davies R.

BMC Bioinformatics. 2012 Apr 27;13:63. doi: 10.1186/1471-2105-13-63.

9.

A graph-theoretic approach for classification and structure prediction of transmembrane β-barrel proteins.

Tran Vdu T, Chassignet P, Sheikh S, Steyaert JM.

BMC Genomics. 2012 Apr 12;13 Suppl 2:S5. doi: 10.1186/1471-2164-13-S2-S5.

10.

Computational studies of membrane proteins: models and predictions for biological understanding.

Liang J, Naveed H, Jimenez-Morales D, Adamian L, Lin M.

Biochim Biophys Acta. 2012 Apr;1818(4):927-41. doi: 10.1016/j.bbamem.2011.09.026. Epub 2011 Oct 12. Review.

11.

Structural plasticity in self-assembling transmembrane β-sheets.

Bishop CM, Wimley WC.

Biophys J. 2011 Aug 17;101(4):828-36. doi: 10.1016/j.bpj.2011.06.059.

12.

Outer membrane proteins can be simply identified using secondary structure element alignment.

Yan RX, Chen Z, Zhang Z.

BMC Bioinformatics. 2011 Mar 17;12:76. doi: 10.1186/1471-2105-12-76.

13.

A folding pathway-dependent score to recognize membrane proteins.

Hadi-Alijanvand H, Rouhani M, Proctor EA, Dokholyan NV, Moosavi-Movahedi AA.

PLoS One. 2011 Mar 1;6(3):e16778. doi: 10.1371/journal.pone.0016778.

14.

A look at arginine in membranes.

Hristova K, Wimley WC.

J Membr Biol. 2011 Jan;239(1-2):49-56. doi: 10.1007/s00232-010-9323-9. Epub 2010 Nov 25. Review.

15.

OMPdb: a database of {beta}-barrel outer membrane proteins from Gram-negative bacteria.

Tsirigos KD, Bagos PG, Hamodrakas SJ.

Nucleic Acids Res. 2011 Jan;39(Database issue):D324-31. doi: 10.1093/nar/gkq863. Epub 2010 Oct 15.

16.

The prediction and characterization of YshA, an unknown outer-membrane protein from Salmonella typhimurium.

Freeman TC Jr, Landry SJ, Wimley WC.

Biochim Biophys Acta. 2011 Jan;1808(1):287-97. doi: 10.1016/j.bbamem.2010.09.008. Epub 2010 Sep 20.

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