U. Doshi

Most-cited papers

Dynamical network of residue–residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation
U. Doshi, M. Holliday, E. Eisenmesser, D. Hamelberg
2016Proceedings of the National Academy of Sciences of the United States of America156 citations Open access
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Protein folding kinetics: barrier effects in chemical and thermal denaturation experiments.
Athi N. Naganathan, U. Doshi, V. Muñoz
2007Journal of the American Chemical Society116 citations Open access
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Reoptimization of the AMBER force field parameters for peptide bond (Omega) torsions using accelerated molecular dynamics.
U. Doshi, D. Hamelberg
2009Journal of Physical Chemistry B89 citations
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Resolving the complex role of enzyme conformational dynamics in catalytic function
U. Doshi, L. McGowan, Safieh Tork Ladani, D. Hamelberg
2012Proceedings of the National Academy of Sciences of the United States of America82 citations Open access
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Dynamics, energetics, and structure in protein folding.
Athi N. Naganathan, U. Doshi, Adam Fung, M. Sadqi +1 more
2006Biochemistry80 citations Open access
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Protein folding rates and stability: how much is there beyond size?
D. de Sancho, U. Doshi, V. Muñoz
2009Journal of the American Chemical Society74 citations
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Towards fast, rigorous and efficient conformational sampling of biomolecules: Advances in accelerated molecular dynamics.
U. Doshi, D. Hamelberg
2015Biochimica et Biophysica Acta54 citations
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Role for the α-helix in aberrant protein aggregation
Rani Kunjithapatham, F. Oliva, U. Doshi, Mar Pérez +2 more
200552 citations
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The Principles of α-Helix Formation: Explaining Complex Kinetics with Nucleation−Elongation Theory
U. Doshi, V. Muñoz
200435 citations
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Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions.
U. Doshi, D. Hamelberg
2012Journal of Chemical Theory and Computation33 citations
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Examining the limits of time reweighting and Kramers' rate theory to obtain correct kinetics from accelerated molecular dynamics.
Yao Xin, U. Doshi, D. Hamelberg
2010Journal of Chemical Physics31 citations
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Extracting Realistic Kinetics of Rare Activated Processes from Accelerated Molecular Dynamics Using Kramers' Theory.
U. Doshi, D. Hamelberg
2011Journal of Chemical Theory and Computation28 citations
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Water's Contribution to the Energetic Roughness from Peptide Dynamics.
Quentin R. Johnson, U. Doshi, Tong-Ye Shen, D. Hamelberg
2010Journal of Chemical Theory and Computation28 citations
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Enhanced molecular dynamics sampling of drug target conformations
Isela G. Rodriguez-Bussey, U. Doshi, D. Hamelberg
2016Biopolymers25 citations Open access
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Atomic-level insights into metabolite recognition and specificity of the SAM-II riboswitch.
U. Doshi, J. M. Kelley, D. Hamelberg
2012RNA: A publication of the RNA Society25 citations Open access
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Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent.
U. Doshi, D. Hamelberg
2014Journal of Physical Chemistry Letters21 citations
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Role for the alpha-helix in aberrant protein aggregation.
Rani Kunjithapatham, F. Oliva, U. Doshi, Mar Pérez +2 more
2005Biochemistry19 citations
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Kinetics of α-helix formation as diffusion on a one-dimensional free energy surface
U. Doshi, V. Muñoz
200417 citations
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The dilemma of conformational dynamics in enzyme catalysis: perspectives from theory and experiment.
U. Doshi, D. Hamelberg
2014Advances in Experimental Medicine and Biology8 citations
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Chapter 2:Kinetics and Mechanisms of α-Helix Formation
U. Doshi
20083 citations
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One-Dimensional Free Energy Surface Models of Protein Folding: Connecting Theory and Experiments
U. Doshi
2007Digital Repository at the University of Maryland (University of Maryland College Park)0 citations Open access
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