Complete Publication List: Jana Shen – Google Scholar
Selected Publications
103. Oh M, Shen M, Liu R, Stavitskaya L*, and Shen J*, Machine Learned Classification of Ligand Intrinsic Activity at Human μ-Opioid Receptor ACS Chem Neuroscience, in revision, 2024
100. Clayton J, Romany A, Matenoglou E, Gathiotis E, Poulikakos PI, and Shen J*, Mechanism of Dimer Selectivity and Binding Cooperativity of BRAF inhibitors eLife, xx, xx, 2024
98. Liu R, Clayton J, Shen M, Bhatnagar S, and Shen J*, Machine Learning Models to Interrogate Proteome-wide Covalent Ligandabilities Directed at Cysteines JACS Au 4: 1374–1384, 2024
96. Romany A, Payne GF, Shen J*, Mechanism of the Temperature-Dependent Self-Assembly and Polymorphism of Chitin Chem Mater 35: 6472–6481, 2023
95. Liu R, Vazquez-Montelongo EA, Ma S*, and Shen J*, Quantum Descriptors for Predicting and Understanding the Structure-Activity Relationships of Covalent Warheads J Chem Inf Model 63: 4912-4923, 2023
92. Mahinthichaichan P, Liu R, Vo QN, Ellis CR, Stavitskaya L*, and Shen J*, Structure-Kinetics Relationships of Opioids from Molecular Dynamics Simulations and Machine Learning J Chem Inf Model 63: 2196–2206, 2023
91. Clayton J, de Oliveira V M, Ibrahim M F, Sun XY, Mahinthichaichan P, Shen M, Hilgenfeld R, Shen J*., Integrative Approach to Dissect the Drug Resistance Mechanism of the H172Y Mutation of SARS-CoV-2 Main Protease J Chem Inf Mode 63: 3521–3533, 2023
89. de Oliveira VM, Liu R, Shen J*, Constant pH Molecular Dynamics Simulations: Current Status and Recent Applications Curr Opin Struct Biol 77: 102498, 2022
83. Liu R, Zhan S, Che Y, Shen J*, Reactivities of the Front Pocket Ncap Cysteines in Human Kinases. J Med Chem 65: 1525-1535, 2022
82. Mahinthichaichan P, Vo Q, Ellis CR, and Shen J*, Kinetics and Mechanism of Fentanyl Dissociation from the mu-Opioid Receptor. JACS Au 1: 2208–2215, 2021
81. Vo QN, Mahinthichaichan P, Shen J*, and Ellis CR*, How μ-opioid receptor recognizes fentanyl. Nat Commun 12: 984, 2021
78. Verma N, Henderson JA, and Shen J*, Proton-Coupled Conformational Activation of SARS Coronavirus Main Proteases and Opportunity for Designing Small-Molecule Broad-Spectrum Targeted Covalent Inhibitors. J Am Chem Soc 142: 21883–21890, 2020
77. Henderson JA, Verma N, Harris R, Liu R, and Shen J*, Assessment of proton-coupled conformational dynamics of SARS and MERS coronavirus papain-like proteases: Implication for designing broad-spectrum antiviral inhibitors. J Chem Phys 153: 115101, 2020
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 16: 3689-3698, 2020
75. Henderson JA, Beckstein O, and Shen J*, Alternative proton-binding site and long-distance coupling in Escherichia coli sodium–proton antiporter NhaA. Proc Natl Acad Sci USA, 117: 25517-25522, 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, ASAP, 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.
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.
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.
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.
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.
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.
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.
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.
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.
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*, 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.
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.