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Items: 1 to 20 of 69

1.

Site-specific amino acid replacement matrices from structurally constrained protein evolution simulations.

Fornasari MS, Parisi G, Echave J.

Mol Biol Evol. 2002 Mar;19(3):352-6. No abstract available.

PMID:
11861895
2.

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
3.
4.

A test of amino acid reversibility.

Smith NG, Eyre-Walker A.

J Mol Evol. 2001 May;52(5):467-9.

PMID:
11443350
5.
6.

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
7.

In vitro evolution of proteins.

Matsuura T, Yomo T.

J Biosci Bioeng. 2006 Jun;101(6):449-56. Review.

PMID:
16935245
8.

Quantifying structural and functional restraints on amino acid substitutions in evolution of proteins.

Chelliah V, Blundell TL.

Biochemistry (Mosc). 2005 Aug;70(8):835-40.

PMID:
16212538
9.

The compositional adjustment of amino acid substitution matrices.

Yu YK, Wootton JC, Altschul SF.

Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15688-93. Epub 2003 Dec 8.

10.

Heterotachy and functional shift in protein evolution.

Philippe H, Casane D, Gribaldo S, Lopez P, Meunier J.

IUBMB Life. 2003 Apr-May;55(4-5):257-65. Review.

11.

Expanding the genetic code.

Wang L, Xie J, Schultz PG.

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

PMID:
16689635
12.
13.

A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny.

Wang HC, Li K, Susko E, Roger AJ.

BMC Evol Biol. 2008 Dec 16;8:331. doi: 10.1186/1471-2148-8-331.

14.

Evaluation of whether accelerated protein evolution in chordates has occurred before, after, or simultaneously with gene duplication.

Johnston CR, O'Dushlaine C, Fitzpatrick DA, Edwards RJ, Shields DC.

Mol Biol Evol. 2007 Jan;24(1):315-23. Epub 2006 Oct 25.

PMID:
17065596
15.

Cloning independent site-directed mutagenesis using total RNA as template.

Nagy ZB, Fehér LZ, Puskás LG.

Biotechniques. 2004 May;36(5):762-4, 766. No abstract available.

PMID:
15152593
16.

Predicting functional divergence in protein evolution by site-specific rate shifts.

Gaucher EA, Gu X, Miyamoto MM, Benner SA.

Trends Biochem Sci. 2002 Jun;27(6):315-21. Review.

PMID:
12069792
17.

Are transversion mutations better? A Mutagenesis Assistant Program analysis on P450 BM-3 heme domain.

Wong TS, Roccatano D, Schwaneberg U.

Biotechnol J. 2007 Jan;2(1):133-42.

PMID:
17183510
18.

The structural basis of molecular adaptation.

Golding GB, Dean AM.

Mol Biol Evol. 1998 Apr;15(4):355-69. Review.

PMID:
9549087
19.

Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences.

Porto M, Roman HE, Vendruscolo M, Bastolla U.

Mol Biol Evol. 2005 Mar;22(3):630-8. Epub 2004 Nov 10. Erratum in: Mol Biol Evol. 2005 Apr;22(4):1159. Mol Biol Evol. 2005 Apr;22(4):1156.

PMID:
15537801
20.

A universal TANGO?

Pande VS.

Nat Biotechnol. 2004 Oct;22(10):1240-1. No abstract available.

PMID:
15470460

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