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Publications

 

Fatmi, M., Ai, R., and Chang, C-E. A., Synergistic regulation and ligand-induced conformational changes of tryptophan synthase. submitted

 

Ai, R., Fatmi, M., and Chang, C-E. A., T-analyst, a program for efficient analysis of protein conformational changes. in preparation

 

Yuhui Cheng, Chang C-E. A., Yu Z., Zhang Y., Leyhk T. S., Holst M. J. and McCammon J. A., Substrate Channeling in the Sulfate Activating Complex: Combined Continuum Modeling and Coarse-grained Brownian Dynamics Studies. Biophysical J. 2008, 95, 4659-4667 [link]

 

Chang, C-E. A., McLaughlin, W., Baron, R., Wang W., McCammon, J. A., Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association Proc. Natl. Acad. Sci. U. S. A. 2008, 105:7456-7461 [link]

 

Chang, C-E. A., Chen, W. and Gilson, M. K., Analysis of the Change in Ligand Entropy upon Protein Binding. Proc. Natl. Acad. Sci. U. S. A. 2007,104:1534-1539 [link]

 

Gorfe A.A.*., Chang C-E. A.*, Ivanov I and McCammon JA Dynamics of acetylcholinesterase tetramer.  Biophysical J. 2007, 94, 1144-1154  [link] (* co-first authors)

 

Chang C-E. A.,  Trylska J., Tozzini V. and McCammon J. A., Binding Pathways of Ligands to HIV-1 Protease: Coarse-grained and Atomistic Simulations. Chemical Biology & Drug Design.2007,69:5-13[link]

 

Tozzini T., Trylska J., Chang C-E. and McCammon J. A., A Coarse-Grained Model for the Dynamcics of Flap Opening in HIV-1 Protease. J. Structural Biology 2007, 157:606-615 [link], [Supplemental Material].

 

Tozzini T., Trylska J., Chang C-E. A. and McCammon J. A., Coarse-grained molecular dynamics study of HIV-1 protease substrate capture and product release. Biophysical J. 2007, 92: 4179-4187  [link].

 

Chen, W., Chang, C-E. and Gilson, M. K., Computational Analysis and Design of Artificial RGD Receptors. J. Am. Chem. Soc. 2006, 128, 4675-4687 [link]

 

Chang C-E., Shen T.,  Trylska J., Tozzini V. and McCammon J. A., Gated Binding of Ligands to HIV-1 Protease: Brownian Dynamics Simulations in a Coarse-Grained Mode. Biophysical J, 2006, 90: 3880-3885 [link]

 

Minh D.D, Chang C-E., Trylska J, Tozzini V, and  McCammon J.A., The Influence of Macromolecular Crowding on HIV-1 Protease Molecular Dynamics. J. Am. Chem. Soc. 2006, 128, 6006-6007 [link]

 

Chang, C-E., Chen, W.  and Gilson, M. K., Evaluating the accuracy of the quasiharmonic approximation. J. of Chemical Theory and Computation, 2005, 1, 1017-1028. [link]

 

Minh, D.L., Bui, J.M., Chang, C-E., Jain T., and McCammon J.A., The Entropic Cost of Protein-Protein Association: A Case Study on Acetylcholinesterase Binding to Fasciculin-2. Biophysical J, 2005, 89:L25-L27. [link]

Chang, C-E. and Gilson, M. K., Free Energy, Entropy, and Induced Fit in Host-Guest Recognition. J. Am. Chem. Soc. 2004, 126, 13156-13164. [link]

 

Chen, W., Chang, C-E. and Gilson, M. K., Calculation of Cyclodextrin Binding Affinities: Energy, Entropy, and Implications for Drug Design. Biophysical J, 2004, 87, 3035-3049. [link]

 

Chang, C.-E and Gilson, M. K., Tork: A Conformational Analysis Method for Molecules and Complexes, J. of Comput Chem, 2003, 24, 1987-1998. [link]

 

DeJong, E. S.*,  Chang, C.-E*., Gilson, M. K., Marino, J. P., Proflavine Acts as a Rev Inhibitor by Targeting the High-Affinity Rev Binding Site of the Rev-Responsive Element of HIV-1, Biochemistry, 2003. 42, 8035-8046. (* co-first authors) [link]

 

Chang, C.-E., Potter, M. J. and Gilson, M. K., Direct Calculation of Conformational Free Energies in All Degrees of Freedom, J. Phys. Chem. B., 2003. 107, 1048-1055. [link] 

 

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