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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