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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.


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.


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.


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.


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.


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.


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.


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.


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.


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

Martin-Galiano AJ, Frishman D.

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


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.


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.


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.


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.


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.


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.


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.


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.


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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