76. Harris RC, Liu R, and Shen J*, Predicting reactive cysteines with implicit-solvent based continuous constant pH molecular dynamics in Amber. J Chem Theory Comput xxx: xxxx-xxxx, 2020.

75. Henderson JA, Beckstein O, and Shen J*, Resolving the second proton-binding site in the E. coli sodium-proton antiporter NhaA. Submitted.

74. Mahinthichaichan P, Tsai CC, Payne, GF and Shen J*, Polyelectrolytes in electric field: disparate conformational behavior along an aminopolysaccharide chain. ACS Omega xxx: xxx-xxx, 2020.

73. Huang YD, Henderson JA and Shen J*, Continuous constant pH molecular dynamics of transmembrane proteins. Methods Mol Biol. in press, 2020

72. Wu S, Shi X, Yan K, Li J, Huynh R, Raub C, Shen J and Payne GF*, Electric cuing of chitosan's mesoscale organization. React Funct Polym 148: 104492, 2020.

71. Harris RC and Shen J*, GPU-accelerated implementation of continuous constant pH molecular dynamics in Amber: pKa predictions with single pH simulations. J Chem Inf Model 59: 4821-4832, 2019.

70. Tsai CC, Yue Z, and Shen J*, 

How electrostatic coupling enables conformational plasticity in a tyrosine kinase.

J Am Chem Soc 141: 15092-15101, 2019.

69. Kim E, Li J, Kang M, Kelly DL, Chen S, Napolitano A, Panzella L, Shi X, Yan K, Wu S, Shen J, Bentley, WE, Payne GF,

Redox is a global biodevice information processing modality.

Proc IEEE: Special Issue on "Molecular Communications and Networking" 107: 1402-1424, 2019. 

68. Liu R, Yue Z, Tsai CC, and Shen J*, 

Assessing lysine and cysteine reactivities for designing targeted covalent kinase inhibitors.

J Am Chem Soc 141: 6553-6560, 2019. 

67. Li J, Wu S, Kim E, Yan K, Liu H, Liu C, Dong H, Qu X, Shi X, Shen J, Bentley, WE, Payne GF*,

Electrobiofabrication: electrically-based fabrication with biologically-derived materials. 

Biofabrication 11: 032002, 2019. 

66. Tsai CC, Payne GF, and Shen J*,  

Exploring pH-responsive, switchable crosslinking mechanisms for programming reconfigurable hydrogels based on aminopolysaccharides.

Chem Mater 30: 8597-8605, 2018. 

65. Henderson JA, Harris RC, Tsai CC, and Shen J*,  

How ligand protonation state controls water in protein-ligand binding. 

J Phys Chem Lett 9: 5440-5444, 2018.

64. Wu S, Yan K, Zhao Y, Tsai CC, Shen J, Bentley WE, Chen Y, Deng H, Du Y, Payne GF* and Shi X*,

Electrical writing onto a dynamically-responsive polysaccharide medium: patterning structure and function into a reconfigurable medium

Adv Funct Mater 28: 1803139 2018.

63. Shen J*.

Zooming in on a multi-drug transporter reveals details of asymmetric protonation.

Proc Natl Acad Sci USA 115: 6080-6082, 2018.

62. D.A. Case, I.Y. Ben-Shalom, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, D. Ghoreishi, M.K. Gilson, H. Gohlke, A.W. Goetz, D. Greene, R Harris, N. Homeyer, S. Izadi, A. Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, D.J. Mermelstein, K.M. Merz, Y. Miao, G. Monard, C. Nguyen, H. Nguyen, I. Omelyan, A. Onufriev, F. Pan, R. Qi, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, C.L. Simmerling, J. Smith, R. Salomon-Ferrer, J. Swails, R.C. Walker, J. Wang, H. Wei, R.M. Wolf, X. Wu, L. Xiao, D.M. York and P.A. Kollman (2018),

AMBER 2018, University of California, San Francisco.

61. Huang YD, Harris RC, Shen J*.

Generalized Born based continuous constant pH molecular dynamics in Amber: implementation, benchmarking, and analysis.

J Chem Inf Model 58:1372-1383, 2018.

60. Huang YD, Yue Z, Tsai CC, Henderson JA, and Shen J*,

Predicting catalytic proton donors and nucleophiles in enzymes: how adding dynamics helps elucidate the structure-function relationships. 

J Phys Chem Lett 9: 1179-1184, 2018.

59. Yue Z and Shen J*,

pH-dependent cooperativity and existence of a dry molten globule in the folding of a mini-protein BBL.

Phys Chem Chem Phys, 20, 3523-3530, 2018.

58. Yan KLiu Y, Zhang JCorrea SOShang WTsai CCBentley WEShen JScarcelli GRaub CBShi XWPayne GF*,

Electrical programming of soft matter: using temporally varying electrical inputs to spatially control self assembly. 

Biomacromolecules 19: 364-373, 2018. 

57. Yue Z, Chen W, Zgurskaya, H, and Shen J*,

Constant pH molecular dynamics reveals how proton release drives the conformational transition of a transmembrane efflux pump. 

J Chem Theory Comput 13: 6405-6414, 2017.


56. Harris RC, Tsai CC, Ellis CR, and Shen J*,

Proton-coupled conformational allostery modulates the inhibitor selectivity for β-secretase.

J Phys Chem Lett 8: 4832-4837, 2017.

55. Tsai CC, Morrow BH, Chen W, Payne GP, and Shen J*,

Towards understanding the environmental control of hydrogel film properties: how salt modulates the flexibility of chitosan chains. 

Macromolecules 50: 5946-5952, 2017.

54. Deredge DJ, Huang W, Huib C, Matsumura H, Yue Z, Moenne-Loccoz P, Shen J, Wintrode PL, and Wilks A*,

Ligand-induced allostery in the interaction of the Pseudomonas aeruginosa heme binding protein with heme oxygenase. 

Proc Natl Acad Sci USA 114:3421-3426, 2017.

53. Ellis CR, Tsai CC, Lin FY, and Shen J*,

Conformational dynamics of cathepsin D and binding to a small-molecule BACE1 inhibitor.

J Comput Chem 38:1260-1269, 2017.

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 water.

J 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.

49. Kim E, Liu Y, Ben-Yoav H, Winkler TE, Yan K, Shi S, Shen J, Kelly DL, Ghodssi R, Bentley WE, and Payne GF*, 

Fusing sensor paradigms to acquire chemical information: an integrative role for smart biopolymeric hydrogels.

Adv Healthcare Mater 5: 2595-2616, 2016.

48. Ellis CR, Tsai CC, Hou XJ, 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 GF, and Shen J*,
Stimuli-responsive self-assembly of polysaccharide through a rugged energy landscape.
J Am Chem Soc 137: 13024-13030, 2015.


45. Chen W, Shi C, and Shen J*,
Nascent beta-hairpin formation of a natively unfolded fragment peptide reveals the role of hydrophobic contacts. 

Biophys J 109: 630-638, 2015.


44. Chen W, Shi C, MacKerell Jr. AD, and Shen J*,
Conformational dynamics of two natively unfolded fragment peptides: Comparison of the AMBER and CHARMM force fields. 

J Phys Chem B 119: 7902-7910, 2015.


43. Kim E, Xing Y, Cheng Y, Wu H-C, Liu Y, Morrow BH, Ben-Yoav H, Ghodssi R, Rubloff GW, Shen J, Bentley WE, Shi X, and Payne GF*,
Chitosan to connect biology to electronics: Fabricating the bio-device interface and communicating across this interface. Polymers 7: 1-46, 2015.


42. Chen W and Shen J*,
Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics.
J Comput Chem 35: 1986-1996, 2014.


41. Morrow BH, Eike DM, Murch BP, Koenig PH, and Shen J*,
Predicting proton titration in cationic micelle and bilayer environments.
J Chem Phys 141: 084714, 2014.


40. Cote Y, Fu IW, Dobson ET, Goldberger JE, Nguyen HD, and Shen J*,
Mechanism of the pH-controlled self-assembly of nanofibers from peptide amphiphiles.
J Phys Chem C 118: 16272-16278, 2014.


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


38. Morrow BH, Koenig PH, and Shen JK*,
Self-Assembly and bilayer-micelle transition of fatty acids studied by replica-exchange constant pH molecular dynamics.
Langmuir 29: 14823-14830, 2013.


37. Chen W, Wallace JA, Yue Z, and Shen JK*,
Introducing titratable water to all-atom molecular dynamics at constant pH.
Biophys J 105: L15-L17, 2013.


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


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


34. Du, L; King, JB; Morrow, BH; Shen, JK; Miller, AN; Cichewicz, RH*,
An uncommon diaryclopentendione metabolite obtained from a preussia typharum isolate procured using an unconventional cultivation approach.
J Nat Prod 75: 1819-1823, 2012.


33. Yi J*, Morrow BH, Campbell ALO, Shen JK*, and Richter-Addo GB*,
Nitric oxide coupling mediated by iron porphyrins: the N–N bond formation step is facilitated by electrons and a proton.
Chem Commun. 48: 9041-9044, 2012.


32. Wang Y, Shen JK*, Schroeder SJ*,
Nucleotide dynamics at the A-site Cleft in the peptidyl transferase Center of H. marismortui 50S ribosomal subunits.
J Phys Chem Lett 3: 1007-1010, 2012.


31. Wallace JA and Shen JK*,
Unraveling a trap-and-trigger mechanism in the pH-sensitive self-assembly of spider silk proteins.
J Phys Chem Lett 3: 658-662, 2012.


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


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


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


27. Wallace JA, Wang Y, Shi C, Pastoor KJ, Nguyen B-L, Xia K, and Shen JK*,
Towards accurate prediction of pKa values for protein internal residues: the importance of conformational relaxation and desolvation energy.
Proteins 79: 3364-3363, 2011.


26. Wang Y, Wallace JA, Koenig PH, and Shen JK*,
Molecular dynamics simulations of ionic and nonionic surfactant micelles with a generalized Born implicit-solvent model.
J Comput Chem 32: 2358, 2011.


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,
Progress in the prediction of pKa values in proteins.
Proteins 79: 3260-3275, 2011.


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


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


22. Shen JK*,
A method to determine residue-specific denatured-state pKa values from analysis of stability changes in single-mutant cycles.
J Am Chem Soc 132: 7258-7259, 2010.


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


20. Xu N, Campbell AOL, Powell DR, Khandogin J*, and Richter-Addo GB*,
A stable hyponitrite-bridged iron porphyrin complex.

J Am Chem Soc 130: 16498-16499, 2009.


19. Wickham JW, Halye J, Kashtanov S, Khandogin J, and Rice CV*,
Revisiting magnesium chelation by teichoic acid with phosphorus solid-state NMR and theoretical calculations.
J Phys Chem B 113: 2177-2183, 2009.


18. Qian J, Khandogin J, West AH, Cook P*,
Evidence for a catalytic dyad in the active site of homocitrate synthase from saccaromyces cerevisiae.
Biochemistry 47: 6851-6858, 2009.


17. Khandogin J*,
Modeling protonation equilibria in biological macromolecules.

In Challenges and Advances in Computational Chemistry and Physics, Springer Verlag, Chapter 10, 261-284, 2009.


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


Before 2008

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


14. Khandogin J, Raleigh DP, and Brooks CL III*,
Folding intermediate in the villin headpiece domain arises from disruption of an N-terminal hydrogen-bonded network.
J Am Chem Soc 129: 3056-3057, 2007.


13. Khandogin J and Brooks CL III*,
Molecular simulations of pH-mediated biological processes.
Annu. Report Comput. Chem., 2007, vol. 3, 3-11, 2007.


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


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


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


9. Gregersen BA, Khandogin J, Thiel W, and York DM*,
Smooth solvation method for d-orbital semiempirical calculations of biological reactions II: application to transphosphorylation thio effects in solution.
J Phys Chem B 109: 9810-9817, 2005.


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


7. Khandogin J and York DM*,
Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods.
Proteins 56: 724-737. 2004.


6. Khandogin J, Musier-Forsyth K, and D. M. York*,
Insights into the regioselectivity and RNA binding affinity of HIV-1 nucleocapsid protein from linear-scaling quantum methods.
J Mol Biol 330: 993-1004,2003.


5. Khandogin J and York DM*,
Quantum mechanical characterization of nucleic acids in solution: a linear-scaling study of charge fluctuations in DNA and RNA.
J Phys Chem B 106: 7693-7703, 2002.


4. Khandogin J, Hu A, and York DM*,
Electronic structure properties of solvated biomolecules: a quantum approach for macromolecular characterization.
J Comput Chem 21: 1562-1571, 2000.


3. Khandogin J and Ziegler T*,
A simple relativistic correction to the nuclear spin-spin coupling constant.
J Phys Chem A 104: 113-120. 2000.


2. Khandogin J and Ziegler T*,
Density functional study of nuclear magnetic resonance spin-spin coupling constants.
Spectrochim Acta A 55: 607-624, 1999.


1. Khandogin Y, Alexeyev AB, Liebermann H-P, Hirsh G, and Buenker RJ*,
Ab initio relativistic CI calculations of the spectroscopic constants and transition probabilities for the low-lying states of the BiOH/HBiO isomers.
J Mol Spectr 186: 22-33,1997.