Home‎ > ‎

Publications (March 2013)


32. Roberts, C. and Chang C-E. A., Ligand binding pathway elucidation for cryptophane host-guest complexes. J. of Chemical Theory and Computation, 2013, in press, [link].


31. Kumar, E. A., Chen, Q., Kizhake, S., Kolar, C., Kang, M., Chang, C-E. A., Borgstahl, G. E. O., and Natarajan, A., The paradox of conformational constraint in the design of Cbl(TKB)-binding peptides. Scientific Reports, 2013, 3:1639 [link].


30. Yaghmaei, S., Roberts, C., Ai, R., Mizwicki, M. T., and Chang C-E. A., Aognist and antagonist binding to the nuclear vitamin D receptor, dynamics, mutation effects and functional implications. In Silico Pharmacology, 2013, 1:2 [link].


29. Huang, Y.-M. M., Kang, M., and Chang C-E. A., Mechanistic insights into phosphopeptide-binding BRCT domains: preorganization, flexibility and phosphate recognition. J. of Physical Chemistry B, 2012, 116,10247-10258 [link] .  


28. Ai, R., and Chang, C-E. A., Ligand-Specific Homology Modeling of Human Cannabinoid (CB1) Receptor. Journal of Molecular Graphics and Modelling. 2012, [link].


27. Huang, Y.M.M, Chen, W., Potter, M. P., and Chang, C-E. A., Insights from Free-Energy Calculations: Protein Conformational Equilibrium, Driving Forces, and Ligand-Binding Modes., Biophysical J., 2012, 103, 342-351 [link].


26. Kang, M., Roberts, C., Cheng, Y. and Chang, C-E. A., Gating and Intermolecular Interactions in Ligand-protein Association: Coarse-grained Modeling of HIV-1 Protease, J. of Chemical Theory and Computation, 2011, 10:3438-3446 [link] .


25. Chang, C-E. A., Ai, R, Gutierres, M., Marsella, M. J., Successful biomedical applications: cannabinoid analogues for therapeutic use. Computer-Aided Drug Design, Methods in Molecular Biology, book editor: Baron, R. 2012, 819, 595-613 [link], [pdf].


24. Huang, Y.M.M and Chang, C-E. A., Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics, BMC Biophysics, 2011, 4, 12-25 [link]


23. Lai, J., Niks, D., Wang, Y., Domratcheva, T., Barends, T. R. M., Schwarz, F., Olsen, R. A., Elliott, D. W., Fatmi, M. Q., Chang, C-E. A., Schlichting, I., Dunn, M. F. and Mueller, L. J., X-ray and NMR Crystallography in an Enzyme Active Site: The Indoline Quinonoid Intermediate in Tryptophan Synthase, J. Am. Chem. Soc., 2011, 133 (1), 4–7 [link]


22. Fatmi, M.Q., Chang, C.E. A. The role of oligomerization and cooperative regulation in protein function: The case of tryptophan synthase. PLos Computational Biology, 2010, 6, e1000994 [link] .


21. Ai, R., Fatmi, M., and Chang, C-E. A., T-Analyst, a program for efficient analysis of protein conformational changes. J Comput Aided Mol Des, 2010. 24, 819-827 [link]


20. Peterson, F. C., Burgie, E. S., Park, S-Y, Jensen, D. R., Weiner, J. J., Bingman, C. A., Chang, C.-E. A, Cutler, S. R.,  Phillips Jr, G. N. and Volkman, B. F., Structural basis for selective activation of ABA receptors., Nature Structural & Molecular Biology, 2010, 17, 1109 – 1113 [link]


19. Fatmi, M., Ai, R., and Chang, C-E. A., Synergistic regulation and ligand-induced conformational changes of tryptophan synthase., Biochemistry, 2009. 48, 9921-9931 [link].


18. Garcia, A., Borchardt, D, Chang, C-E. A. and Marsella, M. J., Thermal Isomerization of Cannabinoid Analogues. J. Am. Chem. Soc, 2009, 131, 16640-16641 [link] .


17. Gorfe, A. A. #, Chang, C-E. A. #*, Ivanov I and McCammon J. A., Dynamics of the Acetylcholinesterase Tetramer. Biophysical J. 2008, 94: 1144-1154. (# co-first authors) [link]


16. Cheng, Y, 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].


15. Chang, C-E. A.*, McLaughlin W. A., Baron R., Wang W., and J. Andrew 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].


Publications before joining UCR


14. Chang, C-E.*, Trylska J., Tozzini T. and McCammon J. A., Binding Pathways of Ligand to HIV-1 Protease: Coarse-grained and Atomistic Simulation, Chemical Biology and Drug Design., 2007, 1: 5-13 [link].


13. Chang, C-E., 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].


12. Trylska J., Tozzini, T., Chang C-E., and McCammon J. A. HIV-1 Protease Substrate Binding and Product Release Pathways Released Pathways Explored with Coarse-grained Molecular Dynamics, Biophysical J. 2007, 92: 4179-4187 [link].


11. Tozzini, T., Trylska J., Chang C-E., and McCammon J. A. Flap Opening Dynamics in HIV-1 Protease Explored with a Coarse-grained Model, J. or Structural Biology, 2007, 157: 606-605 [link].


10. 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].


9. Chang C-E., Shen T., Trylska J., Tozzini T. 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].


8. Chen, W., Chang, C-E., and Gilson, M. K., Concepts in Receptor Optimization: Targeting the Peptide RGD . J. Am. Chem. Soc, 2006, 128: 4675-4687 [link].


7. 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].


6. 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].


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


4. 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].


3. 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].


2. 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].


1. 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].