Keedy DA - Search Results

1

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

Keedy DA. Keedy DA. Proteins. 2015 May;83(5):797-8. doi: 10.1002/prot.24765. Epub 2015 Feb 10. Proteins. 2015. PMID: 25619796

2

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

Hallen MA, Keedy DA, Donald BR. Hallen MA, et al. Among authors: keedy da. Proteins. 2013 Jan;81(1):18-39. doi: 10.1002/prot.24150. Epub 2012 Sep 18. Proteins. 2013. PMID: 22821798 Free PMC article.

3

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. Keedy DA, et al. Proteins. 2009;77 Suppl 9(Suppl 9):29-49. doi: 10.1002/prot.22551. Proteins. 2009. PMID: 19731372 Free PMC article.

4

Conformational variation of proteins at room temperature is not dominated by radiation damage.

Russi S, González A, Kenner LR, Keedy DA, Fraser JS, van den Bedem H. Russi S, et al. Among authors: keedy da. J Synchrotron Radiat. 2017 Jan 1;24(Pt 1):73-82. doi: 10.1107/S1600577516017343. Epub 2017 Jan 1. J Synchrotron Radiat. 2017. PMID: 28009548 Free PMC article.

5

CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites.

Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidman-Duhovny D, Demerdash ON, Mitchell JC, Wells JA, Fraser JS, Sali A. Cimermancic P, et al. Among authors: keedy da. J Mol Biol. 2016 Feb 22;428(4):709-719. doi: 10.1016/j.jmb.2016.01.029. Epub 2016 Feb 5. J Mol Biol. 2016. PMID: 26854760 Free PMC article.

6

Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit.

Keedy DA, Fraser JS, van den Bedem H. Keedy DA, et al. PLoS Comput Biol. 2015 Oct 27;11(10):e1004507. doi: 10.1371/journal.pcbi.1004507. eCollection 2015 Oct. PLoS Comput Biol. 2015. PMID: 26506617 Free PMC article.

7

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. Keedy DA, et al. Structure. 2014 Jun 10;22(6):899-910. doi: 10.1016/j.str.2014.04.016. Epub 2014 May 29. Structure. 2014. PMID: 24882744 Free PMC article.

8

Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography.

Keedy DA, Kenner LR, Warkentin M, Woldeyes RA, Hopkins JB, Thompson MC, Brewster AS, Van Benschoten AH, Baxter EL, Uervirojnangkoorn M, McPhillips SE, Song J, Alonso-Mori R, Holton JM, Weis WI, Brunger AT, Soltis SM, Lemke H, Gonzalez A, Sauter NK, Cohen AE, van den Bedem H, Thorne RE, Fraser JS. Keedy DA, et al. Elife. 2015 Sep 30;4:e07574. doi: 10.7554/eLife.07574. Elife. 2015. PMID: 26422513 Free PMC article.

9

An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering.

Keedy DA, Hill ZB, Biel JT, Kang E, Rettenmaier TJ, Brandão-Neto J, Pearce NM, von Delft F, Wells JA, Fraser JS. Keedy DA, et al. Elife. 2018 Jun 7;7:e36307. doi: 10.7554/eLife.36307. Elife. 2018. PMID: 29877794 Free PMC article.

10

MolProbity: More and better reference data for improved all-atom structure validation.

Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, Verma V, Keedy DA, Hintze BJ, Chen VB, Jain S, Lewis SM, Arendall WB 3rd, Snoeyink J, Adams PD, Lovell SC, Richardson JS, Richardson DC. Williams CJ, et al. Among authors: keedy da. Protein Sci. 2018 Jan;27(1):293-315. doi: 10.1002/pro.3330. Epub 2017 Nov 27. Protein Sci. 2018. PMID: 29067766 Free PMC article.

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