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Items: 1 to 20 of 90

1.

Rampant exchange of the structure and function of extramembrane domains between membrane and water soluble proteins.

Nam HJ, Han SK, Bowie JU, Kim S.

PLoS Comput Biol. 2013;9(3):e1002997. doi: 10.1371/journal.pcbi.1002997. Epub 2013 Mar 21.

2.

Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications.

Cvicek V, Goddard WA 3rd, Abrol R.

PLoS Comput Biol. 2016 Mar 30;12(3):e1004805. doi: 10.1371/journal.pcbi.1004805. eCollection 2016 Mar.

3.

HMMerThread: detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition.

Bradshaw CR, Surendranath V, Henschel R, Mueller MS, Habermann BH.

PLoS One. 2011 Mar 10;6(3):e17568. doi: 10.1371/journal.pone.0017568.

4.

Comparative analysis of membrane protein structure databases.

Shimizu K, Cao W, Saad G, Shoji M, Terada T.

Biochim Biophys Acta Biomembr. 2018 May;1860(5):1077-1091. doi: 10.1016/j.bbamem.2018.01.005. Epub 2018 Jan 10. Review.

5.

Structural imperatives impose diverse evolutionary constraints on helical membrane proteins.

Oberai A, Joh NH, Pettit FK, Bowie JU.

Proc Natl Acad Sci U S A. 2009 Oct 20;106(42):17747-50. doi: 10.1073/pnas.0906390106. Epub 2009 Oct 6.

6.

A novel family of soluble minimal scaffolds provides structural insight into the catalytic domains of integral membrane metallopeptidases.

López-Pelegrín M, Cerdà-Costa N, Martínez-Jiménez F, Cintas-Pedrola A, Canals A, Peinado JR, Marti-Renom MA, López-Otín C, Arolas JL, Gomis-Rüth FX.

J Biol Chem. 2013 Jul 19;288(29):21279-94. doi: 10.1074/jbc.M113.476580. Epub 2013 Jun 3.

7.

On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins.

Forrest LR, Tang CL, Honig B.

Biophys J. 2006 Jul 15;91(2):508-17. Epub 2006 Apr 28.

8.

Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains.

Anantharaman V, Koonin EV, Aravind L.

J Mol Biol. 2001 Apr 13;307(5):1271-92.

PMID:
11292341
9.

A tale of two symmetrical tails: structural and functional characteristics of palindromes in proteins.

Sheari A, Kargar M, Katanforoush A, Arab S, Sadeghi M, Pezeshk H, Eslahchi C, Marashi SA.

BMC Bioinformatics. 2008 Jun 11;9:274. doi: 10.1186/1471-2105-9-274.

11.

Defining the fold space of membrane proteins: the CAMPS database.

Martin-Galiano AJ, Frishman D.

Proteins. 2006 Sep 1;64(4):906-22.

PMID:
16802318
12.

Comparative analysis of the packing topology of structurally important residues in helical membrane and soluble proteins.

Pabuwal V, Li Z.

Protein Eng Des Sel. 2009 Feb;22(2):67-73. doi: 10.1093/protein/gzn074. Epub 2008 Dec 2.

PMID:
19054790
13.

Improving protein structure similarity searches using domain boundaries based on conserved sequence information.

Thompson KE, Wang Y, Madej T, Bryant SH.

BMC Struct Biol. 2009 May 19;9:33. doi: 10.1186/1472-6807-9-33.

14.

Structure of the soluble domain of a membrane-anchored thioredoxin-like protein from Bradyrhizobium japonicum reveals unusual properties.

Capitani G, Rossmann R, Sargent DF, Grütter MG, Richmond TJ, Hennecke H.

J Mol Biol. 2001 Aug 31;311(5):1037-48.

PMID:
11531338
15.

Membrane Proteins Are Dramatically Less Conserved than Water-Soluble Proteins across the Tree of Life.

Sojo V, Dessimoz C, Pomiankowski A, Lane N.

Mol Biol Evol. 2016 Nov;33(11):2874-2884. Epub 2016 Aug 8.

16.

Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin.

Almén MS, Nordström KJ, Fredriksson R, Schiöth HB.

BMC Biol. 2009 Aug 13;7:50. doi: 10.1186/1741-7007-7-50.

17.

Helical packing patterns in membrane and soluble proteins.

Gimpelev M, Forrest LR, Murray D, Honig B.

Biophys J. 2004 Dec;87(6):4075-86. Epub 2004 Oct 1.

18.

Coverage of whole proteome by structural genomics observed through protein homology modeling database.

Yura K, Yamaguchi A, Go M.

J Struct Funct Genomics. 2006 Jun;7(2):65-76. Epub 2006 Dec 5.

19.

The use of soluble protein structures in modeling helical proteins in a layered membrane.

Lee HW, Lee HC, Lee LK, Teber ET, Church WB.

J Biomol Struct Dyn. 2014;32(2):308-18. doi: 10.1080/07391102.2013.765808. Epub 2013 Mar 25.

PMID:
23527746
20.

Structural bioinformatics prediction of membrane-binding proteins.

Bhardwaj N, Stahelin RV, Langlois RE, Cho W, Lu H.

J Mol Biol. 2006 Jun 2;359(2):486-95. Epub 2006 Mar 30.

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