Selected Publications

52. Chen W, Huang YD and Shen J*, Conformational activation of a transmembrane proton channel from constant pH molecular dynamics. J Phys Chem Lett 7: 3961-3966, 2016.

51. Huang YD, Chen W, and Shen J*, Continuous constant pH molecular dynamics with particle-mesh Ewald and titratabe waterJ Chem Theory Comput 12: 5411-5421, 2016.

50. Huang YD, Chen W, Dotson DL, Beckstein O, and Shen J*, Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA. Nat Commun 7:12940, 2016.

48. Ellis CR, Cheng-Chieh Tsai, Xinjun Hou, and Shen J*, Constant pH molecular dynamics reveals pH-modulated binding of two small-molecule BACE1 inhibitors. J Phys Chem Lett 7: 944-949, 2016.

47. Ellis CR and Shen J*, pH-dependent population shift regulates BACE1 activity and inhibition. J Am Chem Soc 137: 9543-9546, 2015.

46. Morrow BH, Payne GP, and Shen J*, Stimuli-responsive self-assembly of polysaccharide through a rugged energy landscape. J Am Chem Soc 137: 13024-13030, 2015.

39.  Chen W, Morrow BH, Shi C, Shen JK*, 2014. Recent development and application of constant pH molecular dynamics. Mol Simul.  Mol Simulat 40: 830-838, 2014.

37.  Chen W, Wallace JA, and Shen JK*, 2013. Introducing Titratable Water to All-Atom Molecular Dynamics at Constant pH. Biophys J 105: L15.

36. Morrow BH, Koenig PH, and Shen JK*, 2012. Atomistic simulations of pH-dependent self-assembly of micelle and bilayer from fatty acids. J Chem Phys 137: 194902.

35. Wallace JA and Shen JK*, 2012.  Charge-leveling co-ions and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.  J Chem Phys 137: 184105.

30. Shi C, Wallace JA, and Shen JK*, 2012. Thermodynamic coupling of protonation and conformational equilibria in proteins: theory and simulation. Biophys J. 102: 1590-1597.

29. Morrow BH, Wang Y, Wallace JA, Koenig PH, and Shen JK*, 2011. Simulating pH titration of a single surfactant in ionic and nonionic micelles. J Phys Chem B 115: 14980-14990.

28. Wallace JA and Shen JK*, 2011. Continuous constant pH molecular dynamics in explicit solvent with pH-based replica exchange. J Chem Theory Comput 7: 2617-2629.

25. Alexov E, Mehler EL, Baker NA, Baptista A, Huang Y, Milletti F, Nielsen JE, Farrell D, Carstensen T, Olsson MHM, Shen JK, Warwicker J, Williams S, Word JM, 2011. Progress in the prediction of pKa values in proteins. Proteins 79: 3260-3275.

24. Wallace JA and Shen JK*, 2010. Probing the strand orientation and registry alignment in the propagation of amyloid fibrils of Ab(16-22). Biochemistry 49:5290-5298.

23. Shen JK*, 2010. Uncovering specific electrostatic interactions in the denatured states of proteins. Biophys J 99: 924-932.

22. Shen JK*, 2010. A method to determine residue-specific denatured-state pKa values from analysis of stability changes in single-mutant cycles. J Am Chem Soc132: 7258-7259.

21. Wallace JA and Shen JK*, 2009. Predicting protein pKa’s with continuous constant pH molecular dynamics, Methods Enzymol 66: 455-475.

20. Xu N, Campbell AOL, Powell DR, Khandogin J*, and Richter-Addo GB*, 2009. A stable hyponitrite-bridged iron porphyrin complex. J Am Chem Soc 130: 16498-16499.

16. Chen J, Brooks CL III*, and Khandogin J, 2008. Recent advances in implicit solvent based methods for biomolecular simulations. Curr Opin Struct Biol 18: 140-148.

12. Khandogin J, Chen J, and Brooks CL III*, 2006. Exploring atomistic details of pH-dependent peptide folding. Proc Natl Acad Sci USA 103: 18546-18550.

15
. Khandogin J and Brooks CL III*, 2007. Linking folding with aggregation in Alzheimer’s beta-amyloid peptides. Proc Natl Acad Sci USA 104: 16880-16885.

11. Khandogin J and Brooks CL III*, 2006. Toward the accurate first-principles prediction of ionization equilibria in proteins. Biochemistry 45: 9363-9373.

10. Khandogin J and Brooks CL III*, 2005. Constant pH molecular dynamics simulation with proton tautomerism. Biophys J 89: 141-157.

8. Khandogin J, Gregersen BA, Thiel W, and York DM*, 2005. Smooth solvation method for d-orbital semiempirical calculations of biological reactions I: implementation. J Phys Chem B 109: 536-556.