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Publications

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]

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]

Chang, C.-E*., DeJong, E. S.*,  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.  Empirical Ligand Discovery and Novel Modeling Techniques. Ph.D Thesis, 2003. [pdf]

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., 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]

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]

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].

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]

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. 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].

Gorfe A.A.*, Chang C-E. A.*, Ivanov I and McCammon JA Dynamics of acetylcholinesterase tetramer.  Biophysical J. 2007, in press  

(* co-first authors)

Oral Presentations

Multiscale Modeling of Biological Systems. Symposium on Multiscale Dynamics of Biomolecules. Academia Sinica, Taipei, Taiwan, 2007.

Multiscale Simulations in Gated Binding of Ligands to HIV-1 Protease, Pharmacology Research Discussion, Fall 2006, University of California, San Diego.

Ligand Configurational Entropy and Protein Binding, 232^th National Meeting of the American Chemical Society, Fall 2006, San Francisco, CA.

Multiscale Simulations in Gated Binding of Ligands to HIV-1 Protease, 232^th National Meeting of the American Chemical Society, Fall 2006, San Francisco, CA.

Modeling Molecular Recognition: from Small Ligand to Large Biomolecular Systems, UCLA, 2006.

Understanding Molecular Recognition: Applications to drug discovery and ligand-receptor binding prediction, University of Delaware, Newark, DE, 2005.

Theory and Modeling of Molecular Recognition in Protein-Ligand and Host-Guest Systems, National Taiwan University, Taipei, Taiwan, 2005.

Free Energy, Entropy, and Induced Fit in Host-Guest Recognition, 228^th National Meeting, of the American Chemical Society, Fall 2004, Philadelphia , PA

Empirical Ligand Discovery and Novel Modeling Techniques, University of Maryland, College Park, Physical Chemistry Seminar, Spring 2003.

Direct Calculation of Molecular Binding Affinities, Symposium on Emerging Technologies in Computational Chemistry, 224^th National Meeting, of the American Chemical Society, Fall 2002, Boston, MA.

Toward Rational Ligand Design: HIV Rev/RRE and Synthetic Chemical Hosts, CARB Seminar Series, Spring 2002, Rockville, MD.

Molecular Modeling in Drug Discovery, Graduate Research Mini-symposium, Spring 2002, College Park, MD

  Poster Presentation

Multiscale Modeling of Biological Systems: All-atom Molecular Dynamics and Coarse-Grained Brownian Dynamics Simulations. Biophysical Society Annual Meeting, Spring 2007, Baltimore, MD

Gated Binding of Ligands to HIV-1 Protease, Protein Society Meeting, 2006, San Diego, CA.  

Modeling Host-Guest Binding: Conformational Search and Calculation of Binding Affinity, 48^th Biophysical Society Annual Meeting, Spring 2004, Baltimore, MD

Empirical Ligand Discovery and Novel Molecular Modeling Techniques, Bioscience Research Workshop, Fall 2003, College Park, MD

New Methods for Conformational Search and Calculation of Molecular Binding Free Energies, 225^th ACS National Meeting, Spring 2003, New Orleans, LA.

Direct Calculation of Molecular Free Energies, 35^th ACS Regional Meeting, Spring 2002, Fairfax, VA.

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