Selected Publication


 (The full list is found here.)

H. Lei, C. Wu, H. Liu, and Y. Duan (2007) "Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations", PNAS, 104(12), 4925-4930

T. Wang and Y. Duan (2007) "Chromophore Channeling in the G-Protein Coupled Receptor Rhodopsin", J. Am. Chem. Soc. (Communication), 129(22), 6970-6971

H.X. Lei and Y. Duan (2007) "Two-stage folding of HP-35 from ab initio simulations", JMB, 370(1), 196-206(cover story)

W. Zhang and Y. Duan (2006) "Grow to Fit Molecular Dynamics (G2FMD): an ab initio method for protein side chain assignment and refinement" PEDS, 19(2), 55-65

H. Lei, C. Wu, Z.-X. Wang and Y. Duan (2006) "Molecular dynamics simulations and free energy analyses on the dimer formation of an amyloidogenic heptamer peptide from human beta2-microglobulin: implication to the protofibril structure", J. Mol. Biol. 356(4), 1049-1063

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

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

Duan Y, Wu C, Chowdhury S, et al. (2003) "A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations" J. Comp. Chem. 24 (16): 1999-2012

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.

Duan, Y., L. Wang, and P. A. Kollman. (1998) "The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation", PNAS, 95(17): 9897-9902