H. Lei, C. Wu, Z.-X. Wang and Y. Duan (2006) \u201cMolecular dynamics simulations and free energy analyses on the dimer formation of an amyloidogenic heptamer peptide from human beta2-microglobulin: implication to the protofibril structure\u201d, J. Mol. Biol. 356(4), 1049-1063<\/p>\n
H. Lei, C. Wu, H. Liu, and Y. Duan (2007) \u201cFolding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations\u201d, PNAS, 104(12), 4925-4930<\/p>\n
T. Wang and Y. Duan (2007) \u201cChromophore Channeling in the G-Protein Coupled Receptor Rhodopsin\u201d, J. Am. Chem. Soc. (Communication), 129(22), 6970-6971<\/p>\n
W. Zhang and Y. Duan (2006) \u201cGrow to Fit Molecular Dynamics (G2FMD): an ab initio method for protein side chain assignment and refinement\u201d Protein Engineering, Design and Selection 19: 55-65;<\/p>\n
C. Wu, H. Lei and Y. Duan (2005) \u201cElongation of Ordered Peptide Aggregate of an Amyloidogenic Hexapeptide (NFGAIL) Observed in Molecular Dynamics Simulations with Explicit Solvent\u201d, J. Am. Chem. Soc. 127(39), 13530-13537<\/p>\n
H.X. Lei and Y. Duan (2007) \u201cTwo-stage folding of HP-35 from ab initio simulations\u201d, JMB, 370(1), 196-206(cover story)<\/p>\n
A. J. Fischer, N. C. Rockwell, A. Y. Jang, L. A. Ernst, A. S. Waggoner,Y. Duan, H. Lei, and J. C. Lagarias, (2005) \u201cMultiple Roles of a Conserved GAF Domain Tyrosine Residue in Cyanobacterial and Plant Phytochromes\u201d, Biochemistry 44(46), 15203-15215<\/p>\n
W. Zhang, C. Wu, and Y. Duan (2005) \u201cConvergence of replica exchange molecular dynamics\u201d, J. Chem. Phys., 123(15), 154105<\/p>\n
M. C. Lee, R. Yang, and Y. Duan, (2005) \u201cComparison between Generalized-Born and Poisson-Boltzmann methods in Physics Based Scoring Functions for Protein Structure Prediction\u201dJ. Mol. Mod. 12, 101-110<\/p>\n
R. Yang, M. C. Lee, H. Yan, and Y. Duan, (2005) \u001cLoop Conformation and Dynamics of the E. coli HPPK Apo-enzyme and Its Binary Complex with MgATP\u001d, Biophys. J., 89(1): 95-106.<\/p>\n
M. C. Lee, J. Deng, J. M. Briggs and Y. Duan, (2005) \u001cLarge Scale Conformational Dynamics of the HIV-1 Integrase Core Domain and its Catalytic Loop Mutants\u001d, Biophys. J., 88: 3133-3146<\/p>\n
Wu, C., H. Lei, and Y. Duan, (2005)\u001cThe role of Phe in the formation of well-ordered oligomers of amyloidogenic hexapeptide (NFGAIL) observed in molecular dynamics simulations with ex-plicit solvent.\u001d Biophys. J. 88(4): 2897-2906<\/p>\n
J. N. Sarakatsannis and Y. Duan, (2005) \u001cStatistical characterization of salt bridges in proteins\u001d, Proteins, 60(4), 732-739<\/p>\n
Chowdhury, H.X. Lei and Y. Duan, (2005) \u001cDenatured state ensemble and early stage of folding of the G29A Mutant of B-domain of protein A: An all atom molecular dynamics study\u001d, J. Phys. Chem., B, 109, 9073-9081<\/p>\n
Wu, C., H.X. Lei, and Y. Duan, (2004)\u001cFormation of partially ordered oligomers of amyloido-genic hexapeptide (NFGAIL) in aqueous solution observed in molecular dynamics simulations.\u001d Biophys. J., 87(5): p. 3000-3009<\/p>\n
Lei, H.X. and Y. Duan, (2004) \u001cThe role of plastic beta-hairpin and weak hydrophobic core in the stability and unfolding of a full sequence design protein.\u001d J. Chem. Phys., 121(23): p. 12104-12111<\/p>\n
Lei, H. and Y. Duan, (2004). \u201cIncorporating intermolecular distance into protein-protein dock-ing\u201d. Prot. Eng., 17(12): p. 837-845<\/p>\n
Wang, Z.X. and Y. Duan, (2004) \u001cSolvation 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.\u001d J. Comp. Chem., 25(14): p. 1699-1716<\/p>\n
W. Zhang, H. Lei, S. Chowdhury and Y. Duan (2004) \u001cFs-21 peptides can form both single helix and helix-turn-helix\u001d, J. Phys. Chem., 108(22): p. 7479-7489<\/p>\n
M. C. Lee and Y. Duan, (2004) \u001cDistinguish Protein Decoys Using a Scoring Function Based on AMBER Force Field, Short Molecular Dynamics Simulations and the Generalized Born Solvent Model\u001d, Proteins, 2004. 55(3): p. 620-634<\/p>\n
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) \u001cA point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechani-cal calculations\u001d, J. Comp. Chem., 24(16) 1999-2012.<\/p>\n
S. Chowdhury, M. Lee, G. Xiong, and Y. Duan, (2003) \u001cab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution\u001d, J. Mol. Biol., 327: (3) 711 \u2013 717<\/p>\n
Duan, Y. and P. A. Kollman, (1998) \u001cPathways to a protein folding intermediate observed in a 1-ms simulation in aqueous solution\u001d, Science, 282, 740-744<\/p>\n","protected":false},"excerpt":{"rendered":"
H. Lei, C. Wu, Z.-X. Wang and Y. Duan (2006) \u201cMolecular dynamics simulations and free energy analyses on the dimer formation of an amyloidogenic heptamer peptide from human beta2-microglobulin: implication to the protofibril structure\u201d, J. Mol. Biol. 356(4), 1049-1063 H. Lei, C. Wu, H. Liu, and Y. Duan (2007) \u201cFolding \u2026 Continue reading