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Daniel Keedy, PhD

TitlePostdoctoral Scholar
SchoolUCSF School of Pharmacy
DepartmentBioengineering
Address600 16th Street
San Francisco CA 94158
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    1. Russi S, González A, Kenner LR, Keedy DA, Fraser JS, van den Bedem H. Conformational variation of proteins at room temperature is not dominated by radiation damage. J Synchrotron Radiat. 2017 Jan 01; 24(Pt 1):73-82. PMID: 28009548.
      View in: PubMed
    2. Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy D, Woldeyes RA, Schneidmann D, Demerdash ON, Mitchell JC, Wells JA, Fraser JS, Sali A. CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites. J Mol Biol. 2016 Feb 22; 428(4):709-19. PMID: 26854760.
      View in: PubMed
    3. Keedy DA, Fraser JS, van den Bedem H. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit. PLoS Comput Biol. 2015 Oct; 11(10):e1004507. PMID: 26506617; PMCID: PMC4624436.
    4. Keedy D, 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. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography. Elife. 2015; 4. PMID: 26422513.
      View in: PubMed
    5. Keedy DA. Conformational and connotational heterogeneity: a surprising relationship between protein structural flexibility and puns. Proteins. 2015 May; 83(5):797-8. PMID: 25619796.
      View in: PubMed
    6. Keedy DA, van den Bedem H, Sivak DA, Petsko GA, Ringe D, Wilson MA, Fraser JS. Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR. Structure. 2014 Jun 10; 22(6):899-910. PMID: 24882744; PMCID: PMC4082491.
    7. Gainza P, Roberts KE, Georgiev I, Lilien RH, Keedy DA, Chen CY, Reza F, Anderson AC, Richardson DC, Richardson JS, Donald BR. OSPREY: protein design with ensembles, flexibility, and provable algorithms. Methods Enzymol. 2013; 523:87-107. PMID: 23422427; PMCID: PMC3692370.
    8. Hallen MA, Keedy DA, Donald BR. Dead-end elimination with perturbations (DEEPer): a provable protein design algorithm with continuous sidechain and backbone flexibility. Proteins. 2013 Jan; 81(1):18-39. PMID: 22821798; PMCID: PMC3491125.
    9. Keedy DA, Georgiev I, Triplett EB, Donald BR, Richardson DC, Richardson JS. The role of local backrub motions in evolved and designed mutations. PLoS Comput Biol. 2012; 8(8):e1002629. PMID: 22876172; PMCID: PMC3410847.
    10. Tyka MD, Keedy DA, André I, Dimaio F, Song Y, Richardson DC, Richardson JS, Baker D. Alternate states of proteins revealed by detailed energy landscape mapping. J Mol Biol. 2011 Jan 14; 405(2):607-18. PMID: 21073878; PMCID: PMC3046547.
    11. Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr. 2010 Jan; 66(Pt 1):12-21. PMID: 20057044; PMCID: PMC2803126.
    12. Keedy DA, Williams CJ, Headd JJ, Arendall WB, Chen VB, Kapral GJ, Gillespie RA, Block JN, Zemla A, Richardson DC, Richardson JS. The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models. Proteins. 2009; 77 Suppl 9:29-49. PMID: 19731372; PMCID: PMC2877634.
    13. Headd JJ, Immormino RM, Keedy DA, Emsley P, Richardson DC, Richardson JS. Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place. J Struct Funct Genomics. 2009 Mar; 10(1):83-93. PMID: 19002604; PMCID: PMC2704614.
    14. Georgiev I, Keedy D, Richardson JS, Richardson DC, Donald BR. Algorithm for backrub motions in protein design. Bioinformatics. 2008 Jul 1; 24(13):i196-204. PMID: 18586714; PMCID: PMC2718647.
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