Elongation of amyloid peptide NFGAIL
C. Wu, H. Lei and Y. Duan (2005) "Elongation of Ordered Peptide Aggregate of an Amyloidogenic Hexapeptide (NFGAIL) Observed in Molecular Dynamics Simulations with Explicit Solvent", J. Am. Chem. Soc. 127(39), 13530-13537

Folding of Trp-cage motif
Chowdhury S, Lee MC, Xiong G, Duan Y. (2003) "Ab initio Folding Simulation of the Trp-cage Mini-protein Approaches NMR Resolution." J. Mol. Biol. 327(3):711-7
Chowdhury, S.; Lee, M. C.; Duan, Y. (2004) "Characterizing the Rate-Limiting Step of Trp-Cage Folding by All-Atom Molecular Dynamics Simulations." ; J. Phys. Chem. B. 108(36): 13855-13865.

Folding of Alanine-based alpha-helix(Ak16)
Chowdhury S, Zhang W, Wu C, Xiong G, Duan Y. "Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an Alanine-Based Peptide." Biopolymers 68(1): 63-75

Zhang W, Lei H. Chowdhury S, Duan Y. (2004) "Fs-21 Peptides Can Form Both Single Helix and Helix-Turn-Helix." J. Phys. Chem. B, 108: 7479-7489

Folding of the villin head piece subdomain
Duan Y. and P. A. Kollman, 1998, "Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution", Science, 282, 740-744.


Initiation of amyloid fibrils (NFGAIL) and the final structure
C. Wu, H. Lei and Y. Duan (2005) “The role of Phe in the formation of well-ordered oligomers of amyloidogenic hexapeptide (NFGAIL) observed in molecular dynamics simulations with explicit solvent”, Biophys. J. 88(4): 2897-2906



Loop dynamics of HIV integrase
Wild-type loop
G140A/G149A double mutant loop
M. C. Lee, J. Deng, J. M. Briggs and Y. Duan (2005) “Large Scale Conformational Dynamics of the HIV-1 Integrase Core Domain and its Catalytic Loop Mutants”, Biophys. J., 88: 3133-3146