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Results: 11

1.

Conformational and connotational heterogeneity: A surprising relationship between protein structural flexibility and puns.

Keedy DA.

Proteins. 2015 May;83(5):797-8. doi: 10.1002/prot.24765. Epub 2015 Feb 10.

PMID:
25619796
2.

Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR.

Keedy DA, van den Bedem H, Sivak DA, Petsko GA, Ringe D, Wilson MA, Fraser JS.

Structure. 2014 Jun 10;22(6):899-910. doi: 10.1016/j.str.2014.04.016. Epub 2014 May 29.

PMID:
24882744
3.

OSPREY: protein design with ensembles, flexibility, and provable algorithms.

Gainza P, Roberts KE, Georgiev I, Lilien RH, Keedy DA, Chen CY, Reza F, Anderson AC, Richardson DC, Richardson JS, Donald BR.

Methods Enzymol. 2013;523:87-107. doi: 10.1016/B978-0-12-394292-0.00005-9.

4.

The role of local backrub motions in evolved and designed mutations.

Keedy DA, Georgiev I, Triplett EB, Donald BR, Richardson DC, Richardson JS.

PLoS Comput Biol. 2012;8(8):e1002629. doi: 10.1371/journal.pcbi.1002629. Epub 2012 Aug 2.

5.

Dead-end elimination with perturbations (DEEPer): a provable protein design algorithm with continuous sidechain and backbone flexibility.

Hallen MA, Keedy DA, Donald BR.

Proteins. 2013 Jan;81(1):18-39. doi: 10.1002/prot.24150. Epub 2012 Sep 18.

6.

Alternate states of proteins revealed by detailed energy landscape mapping.

Tyka MD, Keedy DA, André I, Dimaio F, Song Y, Richardson DC, Richardson JS, Baker D.

J Mol Biol. 2011 Jan 14;405(2):607-18. doi: 10.1016/j.jmb.2010.11.008. Epub 2010 Nov 10.

7.

MolProbity: all-atom structure validation for macromolecular crystallography.

Chen VB, Arendall WB 3rd, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC.

Acta Crystallogr D Biol Crystallogr. 2010 Jan;66(Pt 1):12-21. doi: 10.1107/S0907444909042073. Epub 2009 Dec 21.

8.

The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models.

Keedy DA, Williams CJ, Headd JJ, Arendall WB 3rd, Chen VB, Kapral GJ, Gillespie RA, Block JN, Zemla A, Richardson DC, Richardson JS.

Proteins. 2009;77 Suppl 9:29-49. doi: 10.1002/prot.22551.

9.

Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place.

Headd JJ, Immormino RM, Keedy DA, Emsley P, Richardson DC, Richardson JS.

J Struct Funct Genomics. 2009 Mar;10(1):83-93. doi: 10.1007/s10969-008-9045-8. Epub 2008 Nov 11.

10.

Ultrasonic characterization of human cancellous bone in vitro using three different apparent backscatter parameters in the frequency range 0.6-15.0 mhz.

Hoffmeister BK, Johnson DP, Janeski JA, Keedy DA, Steinert BW, Viano AM, Kaste SC.

IEEE Trans Ultrason Ferroelectr Freq Control. 2008 Jul;55(7):1442-52. doi: 10.1109/TUFFC.2008.819.

PMID:
18986933
11.

Ultrastructures of rabbit corneal stroma: mapping of optical and morphological anisotropies.

Chang EP, Keedy DA, Chien JC.

Biochim Biophys Acta. 1974 May 24;343(3):615-26. No abstract available.

PMID:
4407034
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