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    Kate Stafford, PhD

    TitlePostdoctoral Scholar
    SchoolUCSF School of Pharmacy
    DepartmentBioengineering
    Phone415-514-4233
    vCardDownload vCard

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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Zeiske T, Stafford KA, Palmer AG. Thermostability of Enzymes from Molecular Dynamics Simulations. J Chem Theory Comput. 2016 Jun 14; 12(6):2489-92. PMID: 27123810.
        View in: PubMed
      2. Stafford KA, Trbovic N, Butterwick JA, Abel R, Friesner RA, Palmer AG. Conformational preferences underlying reduced activity of a thermophilic ribonuclease H. J Mol Biol. 2015 Feb 27; 427(4):853-66. PMID: 25550198; PMCID: PMC4349505 [Available on 02/27/16].
      3. Stafford KA, Palmer Iii AG. Evidence from molecular dynamics simulations of conformational preorganization in the ribonuclease H active site. F1000Res. 2014; 3:67. PMID: 25075292; PMCID: PMC4032109.
      4. Stafford KA, Ferrage F, Cho JH, Palmer AG. Side chain dynamics of carboxyl and carbonyl groups in the catalytic function of Escherichia coli ribonuclease H. J Am Chem Soc. 2013 Dec 4; 135(48):18024-7. PMID: 24219366; PMCID: PMC3918730.
      5. Stafford KA, Robustelli P, Palmer AG. Thermal adaptation of conformational dynamics in ribonuclease H. PLoS Comput Biol. 2013; 9(10):e1003218. PMID: 24098095; PMCID: PMC3789780.
      6. Zeiske T, Stafford KA, Friesner RA, Palmer AG. Starting-structure dependence of nanosecond timescale intersubstate transitions and reproducibility of MD-derived order parameters. Proteins. 2013 Mar; 81(3):499-509. PMID: 23161667; PMCID: PMC3557728.
      7. Robustelli P, Stafford KA, Palmer AG. Interpreting protein structural dynamics from NMR chemical shifts. J Am Chem Soc. 2012 Apr 11; 134(14):6365-74. PMID: 22381384; PMCID: PMC3324661.
      8. Eastwood MP, Stafford KA, Lippert RA, Jensen MØ, Maragakis P, Predescu C, Dror RO, Shaw DE. Equipartition and the Calculation of Temperature in Biomolecular Simulations. J Chem Theory Comput. 2010 Jul 13; 6(7):2045-58. PMID: 26615934.
        View in: PubMed
      9. Eastwood MP, Stafford KA, Lippert RA, Jensen MO, Maragakis P, Predescu C, Dror RO, Shaw DE. . Equipartition and the calculation of temperature in biomolecular simulations. J Chem Theory Comput. 2010; 6(7):2045-2058.
      10. Wriggers W, Stafford KA, Shan Y, Piana S, Maragakis P, Lindorff-Larsen K, Miller PJ, Gullingsrud J, Rendleman CA, Eastwood MP, Dror RO, Shaw DE. Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations. J Chem Theory Comput. 2009 Oct 13; 5(10):2595-605. PMID: 26631775.
        View in: PubMed
      11. Wriggers W, Stafford KA, Shan Y, Piana S, Maragakis P, Lindorff-Larsen K, Miller PJ, Gullingsrud J, Rendleman CA, Eastwood MP, Dror RO, Shaw DE. . Automated event detection and activity monitoring in long molecular dynamics simulations. J Chem Theory Comput. 2009; 5(10):2595-2605.
      12. Stephenson BC, Stafford KA, Beers KJ, Blankschtein D. Application of computer simulation free-energy methods to compute the free energy of micellization as a function of micelle composition. 2. Implementation. J Phys Chem B. 2008 Feb 14; 112(6):1641-56. PMID: 18198857.
        View in: PubMed
      13. Stephenson BC, Stafford KA, Beers KJ, Blankschtein D. Application of computer simulation free-energy methods to compute the free energy of micellization as a function of micelle composition. 1. Theory. J Phys Chem B. 2008 Feb 14; 112(6):1634-40. PMID: 18198856.
        View in: PubMed
      14. Tu T, Rendleman CA, Borhani DW, Dror RO, Gullingsrud J, Jensen MO, Klepeis JL, Maragakis P, Miller P, Stafford KA, Shaw DE. . International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2008. A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories. 2008.
      15. Marko AC, Stafford K, Wymore T. Stochastic pairwise alignments and scoring methods for comparative protein structure modeling. J Chem Inf Model. 2007 May-Jun; 47(3):1263-70. PMID: 17391002.
        View in: PubMed
      16. Blanchard BJ, Chen A, Rozeboom LM, Stafford KA, Weigele P, Ingram VM. Efficient reversal of Alzheimer's disease fibril formation and elimination of neurotoxicity by a small molecule. Proc Natl Acad Sci U S A. 2004 Oct 5; 101(40):14326-32. PMID: 15388848; PMCID: PMC521943.
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