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Items: 1 to 20 of 103

1.

The relationship between relative solvent accessibility and evolutionary rate in protein evolution.

Ramsey DC, Scherrer MP, Zhou T, Wilke CO.

Genetics. 2011 Jun;188(2):479-88. doi: 10.1534/genetics.111.128025. Epub 2011 Apr 5.

2.

Modeling coding-sequence evolution within the context of residue solvent accessibility.

Scherrer MP, Meyer AG, Wilke CO.

BMC Evol Biol. 2012 Sep 12;12:179. doi: 10.1186/1471-2148-12-179.

3.
4.

Structural determinants of protein evolution are context-sensitive at the residue level.

Franzosa EA, Xia Y.

Mol Biol Evol. 2009 Oct;26(10):2387-95. doi: 10.1093/molbev/msp146. Epub 2009 Jul 13.

5.

Proportion of solvent-exposed amino acids in a protein and rate of protein evolution.

Lin YS, Hsu WL, Hwang JK, Li WH.

Mol Biol Evol. 2007 Apr;24(4):1005-11. Epub 2007 Jan 29.

6.

Analysis and prediction of RNA-binding residues using sequence, evolutionary conservation, and predicted secondary structure and solvent accessibility.

Zhang T, Zhang H, Chen K, Ruan J, Shen S, Kurgan L.

Curr Protein Pept Sci. 2010 Nov;11(7):609-28.

PMID:
20887256
7.

Quantitative residue-level structure-evolution relationships in the yeast membrane proteome.

Franzosa EA, Xue R, Xia Y.

Genome Biol Evol. 2013;5(4):734-44. doi: 10.1093/gbe/evt039.

8.

Cellular crowding imposes global constraints on the chemistry and evolution of proteomes.

Levy ED, De S, Teichmann SA.

Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20461-6. doi: 10.1073/pnas.1209312109. Epub 2012 Nov 26.

10.

Exploring the evolutionary rate differences of party hub and date hub proteins in Saccharomyces cerevisiae protein-protein interaction network.

Kahali B, Ahmad S, Ghosh TC.

Gene. 2009 Jan 15;429(1-2):18-22. doi: 10.1016/j.gene.2008.09.032. Epub 2008 Oct 10.

PMID:
18973798
11.
12.

Experimental illumination of a fitness landscape.

Hietpas RT, Jensen JD, Bolon DN.

Proc Natl Acad Sci U S A. 2011 May 10;108(19):7896-901. doi: 10.1073/pnas.1016024108. Epub 2011 Apr 4.

13.

Site-specific structural constraints on protein sequence evolutionary divergence: local packing density versus solvent exposure.

Yeh SW, Liu JW, Yu SH, Shih CH, Hwang JK, Echave J.

Mol Biol Evol. 2014 Jan;31(1):135-9. doi: 10.1093/molbev/mst178. Epub 2013 Oct 8.

14.

Linear regression models for solvent accessibility prediction in proteins.

Wagner M, Adamczak R, Porollo A, Meller J.

J Comput Biol. 2005 Apr;12(3):355-69.

PMID:
15857247
15.

Solvent exposure imparts similar selective pressures across a range of yeast proteins.

Conant GC, Stadler PF.

Mol Biol Evol. 2009 May;26(5):1155-61. doi: 10.1093/molbev/msp031. Epub 2009 Feb 20.

16.

A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility.

Huang TT, del Valle Marcos ML, Hwang JK, Echave J.

BMC Evol Biol. 2014 Apr 9;14:78. doi: 10.1186/1471-2148-14-78.

17.

Do amino acid biosynthetic costs constrain protein evolution in Saccharomyces cerevisiae?

Raiford DW, Heizer EM Jr, Miller RV, Akashi H, Raymer ML, Krane DE.

J Mol Evol. 2008 Dec;67(6):621-30. doi: 10.1007/s00239-008-9162-9.

PMID:
18937004
18.

Integrated assessment of genomic correlates of protein evolutionary rate.

Xia Y, Franzosa EA, Gerstein MB.

PLoS Comput Biol. 2009 Jun;5(6):e1000413. doi: 10.1371/journal.pcbi.1000413. Epub 2009 Jun 12.

19.

Amino acid metabolic origin as an evolutionary influence on protein sequence in yeast.

de Bivort BL, Perlstein EO, Kunes S, Schreiber SL.

J Mol Evol. 2009 May;68(5):490-7. doi: 10.1007/s00239-009-9218-5. Epub 2009 Apr 9.

20.

Modeling evolution at the protein level using an adjustable amino acid fitness model.

Dimmic MW, Mindell DP, Goldstein RA.

Pac Symp Biocomput. 2000:18-29.

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