List of Publication


  1. 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
  2. H.X. Lei and Y. Duan (2007) “Two-stage folding of HP-35 from ab initio simulations”, JMB, 370(1), 196-206(cover story)
  3. T. Wang and Y. Duan (2007) “Chromophore Channeling in the G-Protein Coupled Receptor Rhodopsin”, J. Am. Chem. Soc. (Communication), 129(22), 6970-6971
  4. H.X. Lei and Y. Duan (2007) “Improved sampling methods for molecular simulation”,Curr. Op. Struct. Biol. 17(2), 187-191
  5. H.X. Lei and Y. Duan (2007) “Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation”, J. Phys. Chem. B, 111(19); 5458-5463
  6. C. Wu, H.X. Lei, Z.X. Wang, W. Zhang, and Y. Duan (2007) “Dual binding modes of Congo Red to amyloid protofibril surface observed in molecular dynamics simulations”, J. Am. Chem. Soc. 129, 1225-1232
  7. Z.X. Wang, C. Wu, H.X. Lei, and Y. Duan (2007) “Accurate ab initio study on the hydrogen bond pairs in protein secondary structures”, J. Chem. Theory and Comput., in press
  8. G. Ping, S. G. Dastidar, and Y. Duan. (2007) “Statistical properties and kinetics of end-end contact formation of unfolded polypeptides: A systematic molecular dynamics study”, J. Chem. Phys. 126, 045108
  9. H. Liu, S.G. Dastidar, H. Lei, W. Zhang, M.C. Lee and Y. Duan. (2006) “Protein Conformational changes in protein functions.”, in Molecular Modeling of Proteins. Methods in Molecular Biology book series. Human Press Inc, In press
  10. H. Lei and Y. Duan. “Protein Folding and Unfolding by All-atom Molecular Dynamics.”, in Molecular Modeling of Proteins. Methods in Molecular Biology book series. Human Press Inc, In press
  11. Lei, H.X., S.G. Dastidar, and Y. Duan (2006) “Folding Transition State and Denatured State Ensembles of FSD-1 from Folding and Unfolding Simulations”, J. Phys. Chem. B, 110(43), 22001-22008
  12. C. Wu, H.X. Lei, Z.X. Wang, W. Zhang, and Y. Duan (2006) “Phenol red interacts with the protofibril-like oligomers of an amyloidogenic hexapeptide NFGAIL through both hydrophobic and aromatic contacts.”, Biophys. J., 91(10), 3664-3672
  13. Yang LJ, Tan CH, Hsieh MJ, Wang JM, Duan Y, Cieplak P, Caldwell J, Kollman PA, Luo R, (2006) “New-generation amber united-atom force field”, J. Phys. Chem. B 110(26), 13166-13176
  14. Z-X Wang, W. Zhang, C. Wu, H. Lei, P. Cieplak, and Y. Duan, (2006) “Strike a Balance: optimization of backbone torsion parameters of AMBER polarizable force field (ff02pol) for simulations of proteins and peptides”, J. Comp. Chem., 27(6), 781-790
  15. 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
  16. 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
  17. 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
  18. 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
  19. W. Zhang, C. Wu, and Y. Duan (2005) “Convergence of replica exchange molecular dynamics”, J. Chem. Phys., 123(15), 154105
  20. 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
  21. J. N. Sarakatsannis and Y. Duan, (2005) “Statistical characterization of salt bridges in proteins”, Proteins, 60(4), 732-739
  22. Z.-X. Wang and Y. Duan, (2005) “Hydrogen bonds of N-Methylacetamide in solvents: an ab initio study on the direct interaction energies”, J. Theor. & Comp. Chem., 4(Sp), 689-705
  23. 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
  24. 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.
  25. S. 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
  26. C. Wu, H.X. 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
  27. Wu, C., H.X. Lei, and Y. Duan, (2004).“Formation of partially-ordered oligomers of amyloidogenic hexapeptide (NFGAIL) in aqueous solution observed in molecular dynamics simulations”, Biophys. J. 87(5): p. 3000-3009
  28. 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.
  29. Wang, Z. and Y. Duan, (2004) “Solvent effects on alanine dipeptide: a MP2/cc-pVTZ//MP2/6-31G** study on its (F,; Y) energy maps and conformers in the gas phase, ether and water”, J. Comp. Chem., 25(14): p. 1699-1716
  30. 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.
  31. Lei, H. and Y. Duan, (2004). “Incorporating intermolecular distance into protein-protein docking”, Prot. Eng., 17(12): p. 837-845 (cover story).
  32. 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
  33. Lee MC, Duan Y. (2004) “Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model”, Proteins 55(3):620-634
  34. 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
  35. Chowdhury S, Zhang W, Wu C, Xiong G, Duan Y. (2003) “Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an Alanine-Based Peptide”, Biopolymers 68(1): 63-75
  36. 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
  37. Duan, Y. and P. A. Kollman. (2001) “Computational Protein Folding: from lattice to all-atom”, IBM System Journal, 40 (2001) (2): 297-309
  38. Duan, Y., S. C. Harvey, and P. A. Kollman. (2001) “Protein Folding and Beyond”, Chemistry for the 21st Century, E. Keinan & I. Schechter ed, 89-101
  39. Lee, MR, Y.Duan, and P.A. Kollman. (2001) “State of the art in studying protein folding and protein structure predictiopn using molecular dynamics methods”, J. Mol. Graphics & Modelling, 19: (1) 146-149
  40. Wang, L, Y. Duan, P. Stouten, G. V. De Lucca, R. M. Klabe, and P.A. Kollman. (2001) “Does a diol cyclic urea inhibitor of HIV-1 protease bind tighter than its corresponding alcohol form? A study by free energy perturbation and continuum electrostatics calculations”, J. Comp. Aided Mol. Design, 15: (2) 145-156.
  41. Lee, M., Y. Duan, and P. A. Kollman. (2000) “Free energy analysis of tghe folding process of villin headpiece subdomain”, Proteins, 39: (4) 309-316
  42. Kollman, P.A., I. Massova, C. Reyes, B. Kuhn, S. Huo, L. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D.A. Case, and T.E. Cheatham, III. (2000) “Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models”, Acc. Chem. Res., 33(12): p. 889-897.
  43. Chong, L. T., Y. Duan, I. Massova, L. Wang, and P. A. Kollman. (1999) “Molecular dynamics and free energy calculations applied to affinity maturation in antibody 48G7”, PNAS, 96, 14330-14335
  44. Wang, L., Y. Duan, R. Shortle, B. Imperiali, and P. A. Kollman, (1999) “Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures”, Protein Sciences, 8:1292-1304.
  45. 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.
  46. 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
  47. Duan, Y., P. Wilkosz, M. Crowley and J.M. Rosenberg. (1997) “Molecular dynamics simulation study of DNA dodecamer d(CGCGAATTCGCG) in solution: conformation and hydration”, J. Mol. Biol., 272(4) 553-572
  48. Duan, Y., P. Wilkosz, and J. M. Rosenberg. (1996) “Dynamic contributions to the DNA binding entropy in DNA-protein complexes”, J. Mol. Biol. 264(3) 546-555
  49. Duan, Y., S. Kumar, P.A. Kollman, and J.M. Rosenberg. (1995) “Gradient SHAKE: an improved method for constrained energy minimization in macromolecular simulations”, J. Comp. Chem., 16(11): p. 1351-1356
  50. Kumar, S., Y. Duan, P.A. Kollman, and J.M. Rosenberg. (1994) “Molecular dynamics simulations suggest that the EcoRI kink is an example of molecular strain”, J. Biomol. Struct. & Dyn. 12(3): p. 487-525.

Patent

    US Patent (US 11/641,387): Zhang, W. and Y. Duan, “Grow to Fit: A Computational method for Structure Prediction and Refinement”, (Pending)