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Kate Stafford, PhD

TitlePostdoctoral Scholar
SchoolUCSF School of Pharmacy
DepartmentBioengineering
Phone415-514-4233
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    Collapse Research 
    Collapse Research Activities and Funding
    Modeling and docking to de-orphanize the GPCRome
    NIH F32GM113393Apr 1, 2015 - Mar 31, 2018
    Role: Principal Investigator

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    Collapse Publications
    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 K, 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 K, 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 K, 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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