Han Group
Computational Biology and Biophysics Group

Publication

30.Xuehan Jiang, Yang Cao, and Han, W.*(2018)“In Silico Study of Recognition between Aβ40 and Aβ40 Fibril Surfaces: An N-Terminal Helical Recognition Motif and Its Implications for Inhibitor Design” ACS Chem. Neurosci 9, 935.

29.The folding mechanism and key metastable state identification of the PrP127–147 monomer studied by molecular dynamics simulations and Markov state model analysis”  Physical Chemistry Chemical Physics 19, 11249.

28. Yang Cao, Xuehan Jiang, and Han, W.*(2017) “Self-Assembly Pathways of β-Sheet-Rich Amyloid-β(1–40) Dimers: Markov State Model Analysis on Millisecond Hybrid-Resolution Simulations” Journal of Chemical Theory and Computation. 13, 5731. 

27. Shu Li, Wan Zhang, and Han, W.* (2017) “Initial Substrate Binding of γ‑Secretase: The Role of Substrate Flexibility” ACS Chem. Neurosci 8, 1279

26. Julian Deeng, Kwok-Yan Chan, Eli O. van der Sluis, Lukas Bischoff, Otto Berninghausen, Han, W, James Gumbart, Klaus Schulten, Birgitta Beatrix,* and Roland Beckmann.* (2016) “Dynamic behavior of trigger factor on the ribosome” Journal of Molecular Biology 428, 3588

25. Yi Zhang, Lela Vukovic, Till Rudack, Han, W, and Klaus Schulten.* (2016) “Recognition of poly-ubiquitins by the proteasome through protein re-folding guided by electrostatic and hydrophobic interactions” Journal of Physical Chemistry B 120, 8137

24. Jiang, T.; Han, W.; Maduke M.; & Tajkhorshid, E.* (2016) “Molecular Basis for Differential Anion Binding and Proton Coupling in the Cl–/H+ Exchanger ClC-ec1” Journal of the American Chemical Society 138, 3066.

23. Khantwal, C.M.; Abraham S.J.; Han, W.; Jiang T.; Chavan T.S.; Cheng R.C.; Elvington S.M.; Liu C.M.; Mathews I.I.; Stein R.A.; Mchaourab H.S.; Tajkhorshid, E.;* Maduke, M.*  (2016) “Revealing an outward-facing open conformational state in a CLC Cl-/H+ exchange transporter” eLife, e11189.

22. Yu, H.; Han, W.; Ma, W.; Schulten, K.* (2015) “Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation” Journal of Chemical Physics 143, 243142 (co-first author).(Highlighted by F1000 Research)

21. Shen, R.; Han, W.; Fiorin, G.; Islam, S.M.; Schulten, K.; Roux, B.* (2015) “Structural refinement of proteins by restrained molecular dynamics simulations with non-interacting molecular fragments” PLoS Computational Biology 11, e1004368.

20. Han, W.; Schulten, K.* (2014) “Fibril elongation by Aβ(17-42): Kinetic network analysis of hybrid-resolution molecular dynamics simulations” Journal of the American Chemical Society 136, 12450.

19. Han, W.; Cheng, R. C.; Maduke, M. C.;* Tajkhorshid, E.* (2014) “Water access points and hydration pathways in CLC H+/Cl transporters” Proceedings of the National Academy of Science USA 111, 1819 (see the highlight at PNAS 2014, 111, 1668).

18. Sothiselvam, S.; Liu, B.; Han, W.; Ramu, H.; Klepacki, D.; Atkinson, G.; Brauer, A.; Remm, M.; Tenson, T.; Schulten, K.; Vazquez-Laslop, N.;* Mankin, A. S.* (2014) “Macrolide antibiotics predispose the ribosome for programmed translation arrest of regulatory peptides” Proceedings of the National Academy of Science USA 111, 9804.

17. Gamini, R.; Han, W.; Schulten, K.* (2014) “Assembly of Nsp1 nucleoporins provides insight into nuclear pore complex gating” PLoS Computational Biology 10, e1003488.

16. Jo, S.; Cheng, X.; Islam, S.M.; Huang, L.; Rui, H.; Zhu, A.; Lee, H.S.; Qi, Y.; Han, W.; Vanommeslaeghe, K.; MackKerell, A.D.; Roux, B.;* Im, W. *(2014) “CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues” Advances in Protein Chemistry and Structural Biology, 96, 235.

15. Enkavi, G.; Li, J.; Wen, P.; Thangapandian, S.; Moradi, M.; Jiang, T.; Han, W.; Tajkhorshid, E.* (2014) “A microscopic view of the mechanisms of active transporter across the cellular membrane” Annual Reports in Computational Chemistry, 10, 77.

14. Qi, Y.F.; Cheng, X.; Han, W.; Jo, S.; Schulten, K.; Im, W.* (2014) “CHARMM-GUI PACE CG Builder for solution, micelle, and bilayer coarse-grained simulations” Journal of Chemical Information and Modeling 54, 1003.

13. Han, W.; Schulten, K.* (2013) “Characterization of folding mechanisms of Trp-cage and WW-domain by network analysis of simulations with a hybrid-resolution force field” Journal of Physical Chemistry B 117, 13367.

12. Jiang, F.; Han, W.; Wu, Y.-D.* (2013) “The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development” Physical Chemistry Chemical Physics 15, 3413.

11. Han, W.; Schulten, K.* (2012) “Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: improved backbone hydration and interactions between charged side chains” Journal of Chemical Theory and Computation 8, 4413.

10. Wan, C.-K.; Han, W.; Wu, Y.-D.* (2011) “Parameterization of PACE force field for membrane environment and simulation of helical peptides and helix-helix association” Journal of Chemical Theory and Computation 8, 300.

9. Han, W.; Wan, C.-K.; Jiang, F.; Wu, Y.-D.* (2010) “PACE force field for protein simulations. 1. Full parameterization of version 1 and verification” Journal of Chemical Theory and Computation 6, 3373.

8. Han, W.; Wan, C.-K.; Wu, Y.-D.* (2010) “PACE force field for protein simulations. 2. Folding simulations of peptides” Journal of Chemical Theory and Computation 6, 3390.

7. Jiang, F.; Han, W.; Wu, Y.-D.* (2010) “Influence of side chain conformations on local conformational features of amino acids and implication for force field development” Journal of Physical Chemistry B 114, 5840.

6. Wu, Y.-D.;* Han, W.; Wang, D.P.; Gao, Y.; Zhao, Y.L. (2008) “Theoretical analysis of secondary structures of β-peptides” Account of Chemical Research 41, 1418.

5. Han, W.; Wan, C.-K.; Wu, Y.-D.* (2008) “Toward a coarse-grained protein model coupled with a coarse-grained solvent model: solvation free energies of amino acid side chains” Journal of Chemical Theory and Computation 4, 1891.

4. Han, W.; Xiong, H.; Wu, Y.-D.* (2008) “In silico study on the effect of F19T mutation on amyloid-β peptide (10-35)” Frontier in Bioscience 13, 3951.

3. Han, W.; Wu, Y.-D.* (2007) “Molecular dynamics studies of hexamers of amyloid-β peptide (16-35) and its mutants: Influence of charge states on amyloid formation” Proteins 66, 575.

2. Han, W.; Wu, Y.-D.* (2007) “Coarse-grained protein model coupled with a coarse-grained water model: Molecular dynamics study of polyalanine-based peptides” Journal of Chemical Theory and Computation 3, 2146 (co-corresponding author).

1. Han, W.; Wu, Y.-D.* (2005) “A strand-loop-strand structure is a possible intermediate in fibril elongation: Long-time simulations of amyloid-β peptide (10-35)” Journal of the American Chemical Society 127, 15408.