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Papers

  1. Coarse-grained molecular simulations of allosteric cooperativity, Prithviraj Nandigrami and John J. Portman, The Journal of Chemical Physics 144, 105101 (2016). [Abstract]
  2. 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]
  3. Allostery and Folding of the N-Terminal Receiver Domain of Protein NtrC, Swarnendu Tripathi and John J. Portman, J. Phys.Chem. B (2013). [Abstract]
  4. 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]
  5. Cooperativity and protein folding rates, John J. Portman, Curr. Opin. Struct. Biol. 20: 11-15 (2010). [Abstract]
  6. 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]
  7. 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]
  8. Capillarity-like growth of protein folding nuclei, Xianghong Qi and John J. Portman, Proc. Natl. Acad. Sci. USA 105, 11164--11169 (2008) . [Abstract]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  13. 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]
  14. 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]
  15. 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]
  16. 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]
  17. 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]
  18. 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]
  19. 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]