Urmi R. Doshi, Ph.D. - Publications

2007 Biochemistry University of Maryland, College Park, College Park, MD 
General Biophysics, Biochemistry, Bioinformatics Biology

17 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Doshi U, Holliday MJ, Eisenmesser EZ, Hamelberg D. Dynamical network of residue-residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation. Proceedings of the National Academy of Sciences of the United States of America. 113: 4735-40. PMID 27071107 DOI: 10.1073/Pnas.1523573113  0.344
2016 Rodriguez-Bussey IG, Doshi U, Hamelberg D. Enhanced molecular dynamics sampling of drug target conformations. Biopolymers. 105: 35-42. PMID 26352326 DOI: 10.1002/Bip.22740  0.313
2015 Doshi U, Hamelberg D. Towards fast, rigorous and efficient conformational sampling of biomolecules: Advances in accelerated molecular dynamics. Biochimica Et Biophysica Acta. 1850: 878-88. PMID 25153688 DOI: 10.1016/J.Bbagen.2014.08.003  0.33
2014 Doshi U, Hamelberg D. Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent. The Journal of Physical Chemistry Letters. 5: 1217-24. PMID 26274474 DOI: 10.1021/Jz500179A  0.443
2014 Doshi U, Hamelberg D. The dilemma of conformational dynamics in enzyme catalysis: perspectives from theory and experiment. Advances in Experimental Medicine and Biology. 805: 221-43. PMID 24446364 DOI: 10.1007/978-3-319-02970-2_10  0.419
2012 Doshi U, Hamelberg D. Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions. Journal of Chemical Theory and Computation. 8: 4004-12. PMID 26605567 DOI: 10.1021/Ct3004194  0.357
2012 Doshi U, McGowan LC, Ladani ST, Hamelberg D. Resolving the complex role of enzyme conformational dynamics in catalytic function. Proceedings of the National Academy of Sciences of the United States of America. 109: 5699-704. PMID 22451902 DOI: 10.1073/Pnas.1117060109  0.422
2011 Doshi U, Hamelberg D. Extracting Realistic Kinetics of Rare Activated Processes from Accelerated Molecular Dynamics Using Kramers' Theory. Journal of Chemical Theory and Computation. 7: 575-81. PMID 26596291 DOI: 10.1021/Ct1005399  0.404
2010 Johnson Q, Doshi U, Shen T, Hamelberg D. Water's Contribution to the Energetic Roughness from Peptide Dynamics. Journal of Chemical Theory and Computation. 6: 2591-7. PMID 26616063 DOI: 10.1021/Ct100183S  0.43
2010 Xin Y, Doshi U, Hamelberg D. Examining the limits of time reweighting and Kramers' rate theory to obtain correct kinetics from accelerated molecular dynamics. The Journal of Chemical Physics. 132: 224101. PMID 20550384 DOI: 10.1063/1.3432761  0.427
2009 Doshi U, Hamelberg D. Reoptimization of the AMBER force field parameters for peptide bond (Omega) torsions using accelerated molecular dynamics. The Journal of Physical Chemistry. B. 113: 16590-5. PMID 19938868 DOI: 10.1021/Jp907388M  0.398
2009 De Sancho D, Doshi U, Muñoz V. Protein folding rates and stability: how much is there beyond size? Journal of the American Chemical Society. 131: 2074-5. PMID 19170596 DOI: 10.1021/Ja808843H  0.663
2007 Naganathan AN, Doshi U, Muñoz V. Protein folding kinetics: barrier effects in chemical and thermal denaturation experiments. Journal of the American Chemical Society. 129: 5673-82. PMID 17419630 DOI: 10.1021/Ja0689740  0.682
2006 Naganathan AN, Doshi U, Fung A, Sadqi M, Muñoz V. Dynamics, energetics, and structure in protein folding. Biochemistry. 45: 8466-75. PMID 16834320 DOI: 10.1021/Bi060643C  0.684
2005 Kunjithapatham R, Oliva FY, Doshi U, Pérez M, Avila J, Muñoz V. Role for the alpha-helix in aberrant protein aggregation. Biochemistry. 44: 149-56. PMID 15628855 DOI: 10.1021/Bi048564T  0.548
2004 Doshi UR, Munoz V. The Principles of α-Helix Formation: Explaining Complex Kinetics with Nucleation−Elongation Theory Journal of Physical Chemistry B. 108: 8497-8506. DOI: 10.1021/Jp049896A  0.557
2004 Doshi U, Muñoz V. Kinetics of α-helix formation as diffusion on a one-dimensional free energy surface Chemical Physics. 307: 129-136. DOI: 10.1016/J.Chemphys.2004.05.022  0.607
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