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Items: 1 to 20 of 52

1.

An efficient algorithm for multistate protein design based on FASTER.

Allen BD, Mayo SL.

J Comput Chem. 2010 Apr 15;31(5):904-16. doi: 10.1002/jcc.21375.

PMID:
19637210
2.

Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details.

Potapov V, Cohen M, Schreiber G.

Protein Eng Des Sel. 2009 Sep;22(9):553-60. doi: 10.1093/protein/gzp030. Epub 2009 Jun 26.

PMID:
19561092
3.

X-ray vs. NMR structures as templates for computational protein design.

Schneider M, Fu X, Keating AE.

Proteins. 2009 Oct;77(1):97-110. doi: 10.1002/prot.22421.

4.

Design of protein-interaction specificity gives selective bZIP-binding peptides.

Grigoryan G, Reinke AW, Keating AE.

Nature. 2009 Apr 16;458(7240):859-64. doi: 10.1038/nature07885.

5.

Protein design by directed evolution.

Jäckel C, Kast P, Hilvert D.

Annu Rev Biophys. 2008;37:153-73. doi: 10.1146/annurev.biophys.37.032807.125832. Review.

PMID:
18573077
6.

Design of protein-ligand binding based on the molecular-mechanics energy model.

Boas FE, Harbury PB.

J Mol Biol. 2008 Jul 4;380(2):415-24. doi: 10.1016/j.jmb.2008.04.001. Epub 2008 Apr 8.

7.

Kemp elimination catalysts by computational enzyme design.

Röthlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O, Albeck S, Houk KN, Tawfik DS, Baker D.

Nature. 2008 May 8;453(7192):190-5. doi: 10.1038/nature06879. Epub 2008 Mar 19.

PMID:
18354394
8.

De novo computational design of retro-aldol enzymes.

Jiang L, Althoff EA, Clemente FR, Doyle L, Röthlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF 3rd, Hilvert D, Houk KN, Stoddard BL, Baker D.

Science. 2008 Mar 7;319(5868):1387-91. doi: 10.1126/science.1152692.

9.

Advances in laboratory evolution of enzymes.

Bershtein S, Tawfik DS.

Curr Opin Chem Biol. 2008 Apr;12(2):151-8. doi: 10.1016/j.cbpa.2008.01.027. Epub 2008 Mar 7. Review.

PMID:
18284924
10.

The point mutation A34F causes dimerization of GB1.

Jee J, Byeon IJ, Louis JM, Gronenborn AM.

Proteins. 2008 May 15;71(3):1420-31.

PMID:
18076051
11.

High-resolution design of a protein loop.

Hu X, Wang H, Ke H, Kuhlman B.

Proc Natl Acad Sci U S A. 2007 Nov 6;104(45):17668-73. Epub 2007 Oct 30.

12.

Progress in computational protein design.

Lippow SM, Tidor B.

Curr Opin Biotechnol. 2007 Aug;18(4):305-11. Epub 2007 Jul 20. Review.

13.

Modeling backbone flexibility to achieve sequence diversity: the design of novel alpha-helical ligands for Bcl-xL.

Fu X, Apgar JR, Keating AE.

J Mol Biol. 2007 Aug 24;371(4):1099-117. Epub 2007 May 5.

14.

Computing van der Waals energies in the context of the rotamer approximation.

Grigoryan G, Ochoa A, Keating AE.

Proteins. 2007 Sep 1;68(4):863-78.

PMID:
17554777
15.

Eris: an automated estimator of protein stability.

Yin S, Ding F, Dokholyan NV.

Nat Methods. 2007 Jun;4(6):466-7. No abstract available.

PMID:
17538626
16.

Computational protein design promises to revolutionize protein engineering.

Alvizo O, Allen BD, Mayo SL.

Biotechniques. 2007 Jan;42(1):31, 33, 35 passim.

17.

Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function.

Treynor TP, Vizcarra CL, Nedelcu D, Mayo SL.

Proc Natl Acad Sci U S A. 2007 Jan 2;104(1):48-53. Epub 2006 Dec 19.

18.

Combinatorial methods for small-molecule placement in computational enzyme design.

Lassila JK, Privett HK, Allen BD, Mayo SL.

Proc Natl Acad Sci U S A. 2006 Nov 7;103(45):16710-5. Epub 2006 Oct 30.

19.

Dramatic performance enhancements for the FASTER optimization algorithm.

Allen BD, Mayo SL.

J Comput Chem. 2006 Jul 30;27(10):1071-5.

PMID:
16685715
20.

Computational design of a single amino acid sequence that can switch between two distinct protein folds.

Ambroggio XI, Kuhlman B.

J Am Chem Soc. 2006 Feb 1;128(4):1154-61.

PMID:
16433531

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