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Items: 1 to 20 of 98

1.

Analyzing site heterogeneity during protein evolution.

Koshi JM, Goldstein RA.

Pac Symp Biocomput. 2001:191-202.

2.

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.

4.
5.

Models of natural mutations including site heterogeneity.

Koshi JM, Goldstein RA.

Proteins. 1998 Aug 15;32(3):289-95.

6.

A new formulation of protein evolutionary models that account for structural constraints.

Bordner AJ, Mittelmann HD.

Mol Biol Evol. 2014 Mar;31(3):736-49. doi: 10.1093/molbev/mst240. Epub 2013 Dec 3.

PMID:
24307688
7.

Protein map: an alignment-free sequence comparison method based on various properties of amino acids.

Yu C, Cheng SY, He RL, Yau SS.

Gene. 2011 Oct 15;486(1-2):110-8. doi: 10.1016/j.gene.2011.07.002. Epub 2011 Jul 19.

PMID:
21803133
8.
9.

ProtTest: selection of best-fit models of protein evolution.

Abascal F, Zardoya R, Posada D.

Bioinformatics. 2005 May 1;21(9):2104-5. Epub 2005 Jan 12.

PMID:
15647292
10.

Protein evolution within and between species.

Schmitt AO, Schuchhardt J, Ludwig A, Brockmann GA.

J Theor Biol. 2007 Nov 21;249(2):376-83. Epub 2007 Aug 8.

PMID:
17881006
11.

The tangled bank of amino acids.

Goldstein RA, Pollock DD.

Protein Sci. 2016 Jul;25(7):1354-62. doi: 10.1002/pro.2930. Epub 2016 May 12.

12.

Modeling protein evolution with several amino acid replacement matrices depending on site rates.

Le SQ, Dang CC, Gascuel O.

Mol Biol Evol. 2012 Oct;29(10):2921-36. Epub 2012 Apr 6.

PMID:
22491036
13.

Bayesian semiparametric regression models to characterize molecular evolution.

Datta S, Rodriguez A, Prado R.

BMC Bioinformatics. 2012 Oct 30;13:278. doi: 10.1186/1471-2105-13-278.

14.

Expanding the genetic code.

Wang L, Xie J, Schultz PG.

Annu Rev Biophys Biomol Struct. 2006;35:225-49. Review.

PMID:
16689635
15.

Evolution encoded.

Freeland SJ, Hurst LD.

Sci Am. 2004 Apr;290(4):84-91. No abstract available.

PMID:
15045758
16.

What amino acid properties affect protein evolution?

Xia X, Li WH.

J Mol Evol. 1998 Nov;47(5):557-64.

PMID:
9797406
17.

Codon substitution models based on residue similarity and their applications.

Liu X, Liu H, Guo W, Yu K.

Gene. 2012 Nov 1;509(1):136-41. doi: 10.1016/j.gene.2012.07.075. Epub 2012 Aug 10.

PMID:
22902303
18.

Prediction of contacts from correlated sequence substitutions.

Taylor WR, Hamilton RS, Sadowski MI.

Curr Opin Struct Biol. 2013 Jun;23(3):473-9. doi: 10.1016/j.sbi.2013.04.001. Epub 2013 May 14. Review.

PMID:
23680395
19.

Selecton: a server for detecting evolutionary forces at a single amino-acid site.

Doron-Faigenboim A, Stern A, Mayrose I, Bacharach E, Pupko T.

Bioinformatics. 2005 May 1;21(9):2101-3. Epub 2005 Jan 12.

PMID:
15647294
20.

Comparing models of evolution for ordered and disordered proteins.

Brown CJ, Johnson AK, Daughdrill GW.

Mol Biol Evol. 2010 Mar;27(3):609-21. doi: 10.1093/molbev/msp277. Epub 2009 Nov 18. Erratum in: Mol Biol Evol. 2012 Jan;29(1):443.

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