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1

Protein Folding Rates and Stability: How Much Is There Beyond Size?

De Sancho, David, Doshi, Urmi, Muñoz, Victor

Journal:

Journal of the American Chemical Society

Year:

2009

Language:

english

File:

PDF, 511 KB

english, 2009

2

Kinetics of α-helix formation as diffusion on a one-dimensional free energy surface

Urmi Doshi, Victor Muñoz

Journal:

Chemical Physics

Year:

2004

Language:

english

File:

PDF, 456 KB

english, 2004

3

Dynamics, Energetics, and Structure in Protein Folding †

Naganathan, Athi N., Doshi, Urmi, Fung, Adam, Sadqi, Mourad, Muñoz, Victor

Journal:

Year:

2006

Language:

english

File:

PDF, 167 KB

english, 2006

4

Role for the α-Helix in Aberrant Protein Aggregation †

Kunjithapatham, Rani, Oliva, Fabiana Y., Doshi, Urmi, Pérez, Mar, Ávila, Jesus, Muñoz, Victor

Journal:

Year:

2005

Language:

english

File:

PDF, 662 KB

english, 2005

5

Protein Folding Kinetics: Barrier Effects in Chemical and Thermal Denaturation Experiments

Naganathan, Athi N., Doshi, Urmi, Muñoz, Victor

Journal:

Journal of the American Chemical Society

Year:

2007

Language:

english

File:

PDF, 417 KB

english, 2007

6

Extracting Realistic Kinetics of Rare Activated Processes from Accelerated Molecular Dynamics Using Kramers’ Theory

Doshi, Urmi, Hamelberg, Donald

Journal:

Journal of Chemical Theory and Computation

Year:

2011

Language:

english

File:

PDF, 1.71 MB

english, 2011

7

The Principles of α-Helix Formation: Explaining Complex Kinetics with Nucleation−Elongation Theory

Doshi, Urmi R., Muñoz, Victor

Journal:

Journal of Physical Chemistry B

Year:

2004

Language:

english

File:

PDF, 219 KB

english, 2004

8

Water’s Contribution to the Energetic Roughness from Peptide Dynamics

Johnson, Quentin, Doshi, Urmi, Shen, Tongye, Hamelberg, Donald

Journal:

Journal of Chemical Theory and Computation

Year:

2010

Language:

english

File:

PDF, 2.82 MB

english, 2010

9

Reoptimization of the AMBER Force Field Parameters for Peptide Bond (Omega) Torsions Using Accelerated Molecular Dynamics

Doshi, Urmi, Hamelberg, Donald

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 822 KB

english, 2009

10

Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent

Doshi, Urmi, Hamelberg, Donald

Journal:

The Journal of Physical Chemistry Letters

Year:

2014

Language:

english

File:

PDF, 2.81 MB

english, 2014

11

Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions

Doshi, Urmi, Hamelberg, Donald

Journal:

Journal of Chemical Theory and Computation

Year:

2012

Language:

english

File:

PDF, 4.92 MB

english, 2012

12

Towards fast, rigorous and efficient conformational sampling of biomolecules: Advances in accelerated molecular dynamics

Doshi, Urmi, Hamelberg, Donald

Journal:

Biochimica et Biophysica Acta (BBA) - General Subjects

Year:

2015

Language:

english

File:

PDF, 2.27 MB

english, 2015

13

Examining the limits of time reweighting and Kramers’ rate theory to obtain correct kinetics from accelerated molecular dynamics

Xin, Yao, Doshi, Urmi, Hamelberg, Donald

Journal:

The Journal of Chemical Physics

Year:

2010

Language:

english

File:

PDF, 748 KB

english, 2010

14

Dynamical network of residue–residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation

Doshi, Urmi, Holliday, Michael J., Eisenmesser, Elan Z., Hamelberg, Donald

Journal:

Proceedings of the National Academy of Sciences

Year:

2016

Language:

english

File:

PDF, 1.26 MB

english, 2016

15

Enhanced molecular dynamics sampling of drug target conformations

Rodriguez-Bussey, Isela G., Doshi, Urmi, Hamelberg, Donald, McCammon, J.

Journal:

Year:

2016

Language:

english

File:

PDF, 516 KB

english, 2016

16

Indexing of exoplanets in search for potential habitability: application to Mars-like worlds

Kashyap Jagadeesh, Madhu, Gudennavar, Shivappa B., Doshi, Urmi, Safonova, Margarita

Journal:

Astrophysics and Space Science

Year:

2017

Language:

english

File:

PDF, 2.15 MB

english, 2017

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