Yong Duan

image of Yong Duan

Associate Professor


UC Davis Genome Center
Bioinformatics Program
Applied Science

Offices and Labs

4335 GBSF
+1 530 754 7632


1996 PhD Physics University of Pittsburgh

Department and Center Affiliations

Applied Science
Genome Center and Bioinformatics Program


Biophysical Society
American Chemical Society

CBS Grad Group Affiliations



5/21/2010 9:26:34 AM
  • 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
  • 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
  • W. Zhang and Y. Duan (2006) "Grow to Fit Molecular Dynamics (G2FMD): an ab initio method for protein side chain assignment and refinement" Protein Engineering, Design and Selection 19: 55-65;
  • 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
  • H.X. Lei and Y. Duan (2007) "Two-stage folding of HP-35 from ab initio simulations", JMB, 370(1), 196-206(cover story)
  • A. J. Fischer, N. C. Rockwell, A. Y. Jang, L. A. Ernst, A. S. Waggoner,Y. Duan, H. Lei, and J. C. Lagarias, (2005) "Multiple Roles of a Conserved GAF Domain Tyrosine Residue in Cyanobacterial and Plant Phytochromes", Biochemistry 44(46), 15203-15215
  • W. Zhang, C. Wu, and Y. Duan (2005) "Convergence of replica exchange molecular dynamics", J. Chem. Phys., 123(15), 154105
  • M. C. Lee, R. Yang, and Y. Duan, (2005) "Comparison between Generalized-Born and Poisson-Boltzmann methods in Physics Based Scoring Functions for Protein Structure Prediction" J. Mol. Mod. 12, 101-110
  • R. Yang, M. C. Lee, H. Yan, and Y. Duan, (2005) Loop Conformation and Dynamics of the E. coli HPPK Apo-enzyme and Its Binary Complex with MgATP, Biophys. J., 89(1): 95-106.
  • 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
  • Wu, C., 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 ex-plicit solvent. Biophys. J. 88(4): 2897-2906
  • J. N. Sarakatsannis and Y. Duan, (2005) Statistical characterization of salt bridges in proteins, Proteins, 60(4), 732-739
  • . Chowdhury, H.X. Lei and Y. Duan, (2005) Denatured state ensemble and early stage of folding of the G29A Mutant of B-domain of protein A: An all atom molecular dynamics study, J. Phys. Chem., B, 109, 9073-9081
  • Wu, C., H.X. Lei, and Y. Duan, (2004)Formation of partially ordered oligomers of amyloido-genic hexapeptide (NFGAIL) in aqueous solution observed in molecular dynamics simulations. Biophys. J., 87(5): p. 3000-3009
  • Lei, H.X. and Y. Duan, (2004) The role of plastic beta-hairpin and weak hydrophobic core in the stability and unfolding of a full sequence design protein. J. Chem. Phys., 121(23): p. 12104-12111
  • Lei, H. and Y. Duan, (2004). "Incorporating intermolecular distance into protein-protein dock-ing". Prot. Eng., 17(12): p. 837-845
  • Wang, Z.X. and Y. Duan, (2004) Solvation effects on alanine dipeptide: A MP2/cc-pVTZ//MP2/6-31G** study of (Phi, Psi) energy maps and conformers in the gas phase, ether, and water. J. Comp. Chem., 25(14): p. 1699-1716
  • W. Zhang, H. Lei, S. Chowdhury and Y. Duan (2004) Fs-21 peptides can form both single helix and helix-turn-helix, J. Phys. Chem., 108(22): p. 7479-7489
  • M. C. Lee and Y. Duan, (2004) Distinguish Protein Decoys Using a Scoring Function Based on AMBER Force Field, Short Molecular Dynamics Simulations and the Generalized Born Solvent Model, Proteins, 2004. 55(3): p. 620-634
  • Y. Duan, C. Wu, S. Chowdhury, M. C. Lee, G. Xiong, W. Zhang, R. Yang, P. Cieplak, R. Luo, T. Lee, J. Caldwell, J. Wang, and P. A. Kollman (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechani-cal calculations, J. Comp. Chem., 24(16) 1999-2012.
  • S. Chowdhury, M. Lee, G. Xiong, and Y. Duan, (2003) ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution, J. Mol. Biol., 327: (3) 711 - 717
  • Duan, Y. and P. A. Kollman, (1998) Pathways to a protein folding intermediate observed in a 1-ms simulation in aqueous solution, Science, 282, 740-744