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Papers
- Coarse-grained molecular simulations of allosteric
cooperativity, Prithviraj Nandigrami and John J. Portman,
The Journal of Chemical Physics 144, 105101 (2016).
[Abstract]
- P. Nandigrami and J. J. Portman: Comparing allosteric
transitions in the domains of calmodulin through
coarse-grained simulations, Prithviraj Nandigrami and John
J. Portman, The Journal of Chemical Physics 144, 105102
(2016).
[Abstract]
- Allostery and Folding of the N-Terminal Receiver Domain of Protein NtrC,
Swarnendu Tripathi and John J. Portman,
J. Phys.Chem. B
(2013).
[Abstract]
- Conformational flexibility and the mechanisms of
allosteric transitions in topologically simlar
proteins, Swarnendu Tripathi and John J. Portman,
J. Chem. Phys. 135, 075104
(2011).
[Abstract]
- Cooperativity and protein folding rates, John
J. Portman,
Curr. Opin. Struct. Biol. 20: 11-15
(2010). [Abstract]
- Inherrent flexibility determines the transition mechanisms of the
EF-hands of Calmodulin, Swarnendu Tripathi and John J. Portman,
Proc. Natl. Acad. Sci. USA 106, 2104--2109
(2009). [Abstract]
- Inherent flexibility and protein function: the
open/closed conformational transition of the
N-terminal domain of calmodulin, Swarnendu Tripathi
and John J. Portman,
J. Chem. Phys. 128, 205104
(2008). [Abstract]
- Capillarity-like growth of protein folding
nuclei, Xianghong Qi and John J. Portman,
Proc. Natl. Acad. Sci. USA 105, 11164--11169
(2008)
. [Abstract]
- Variationally determined free energy profiles for
structural models of proteins: Characteristic
Temperatures for folding and trapping,Tongye Shen,
Chenghang Zong, John J. Portman, and Peter G. Wolynes,
J. Phys. Chem. B, 112 (19), 6074-6082
(2008). [Abstract]
- Excluded volume, local structural cooperativity,
and the polymer physics of protein folding rates,
Xianghong Qi and John J. Portman,
Proc. Natl. Acad. Sci. USA 104, 10841--10846
(2007). [Abstract]
- Peptide Folding Simulations, S. Gnanakaran, Hugh
Nymeyer, John Portman, Kevin Y. Sanbonmatsu, and Angel
E. Garcia,
Curr. Opin. Struct. Biol. 13(2),
168--174
(2003).
[Abstract]
- Non-Gaussian Dynamics from a Simulation of a Short
Peptide: Loop Closure rates and Effective Diffusion
Coefficients, John J. Portman,
J. Chem. Phys. 118, 2381--2391
(2003). [Abstract]
- Microscopic Theory of Protein Folding Rates.II:
Local Reaction Coordinates and Chain Dynamics, John
J. Portman, Shoji Takada, and Peter G. Wolynes,
J. Chem. Phys. 114, 5082--5096
(2001). [Abstract]
- Microscopic Theory of Protein Folding Rates.I:
Fine Structure of the Free Energy Profile and
Folding Routes from a Variational Approach, John
J. Portman, Shoji Takada, and Peter G.Wolynes,
J. Chem. Phys. 144, 5069--5081
(2001). [Abstract]
- Speeding Molecular Recognition by Using the
Folding Funnel: The Fly-casting Mechanism, Benjamin
A.Shoemaker, John J.Portman, and Peter G. Wolynes,
Proc. Natl. Acad. Sci. USA 97, 8868--8873
(2000). [Abstract]
- Complementary Variational Approximations for
Intermittency and Reaction Dynamics in Fluctuating
Environments, John J. Portman and Peter G. Wolynes,
J. Phys. Chem. A 103,10602--10610
(1999). [Abstract]
- Variational Theory of Site Resolved Protein
Folding Free Energy Surfaces, J. J . Portman,
S. Takada, P.~ G. Wolynes,
Phys. Rev. Lett. 81(23), 5237--5240
(1998). [Abstract]
- An Elementary Mode Coupling Theory of Random
Heteropolymer Dynamics, Shoji Takada, John J. Portman,
Peter G. Wolynes,
Proc. Natl. Acad. Sci. USA 94, 2318
(1997). [Abstract]
- Theoretical Investigations of Collisions of
Aligned Atoms: $Ca(4s4f^1F)$ + He, A.~P. Hickman,
J.~J. Portman, S. Krebs, and W. Meyer,
Phys. Rev. Lett. 72 (12), 1814--1818
(1994). [Abstract]