Liu R and Shen J*,
Development and validation of machine learning models based on publicly
available databases for predicting small molecule pKa ’s.
In preparation.
Liu R and Shen J*,
Extensive validation of histidine pKa
predictions with continuous constant pH molecular dynamics in Amber.
In preparation.
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.
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.
Liu R, Verma N, Henderson JA, Zhan S, and Shen J*,
Profiling Cysteines in MAP Kinases for Targeted Covalent Inhibitor Design.
RSC Med Chem, ASAP, 2021.
Liu R, Zhan S, Che Y, Shen J*,
Reactivities of the Front Pocket Ncap Cysteines in Human Kinases.
J Med Chem, ASAP, 2021.
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.
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.
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.
Case, D. A.; Ben-Shalom, I. Y.; Brozell, S. R.; Cerutti, D. S.; Cheatham,
T., III; Cruzeiro, V. W. D.; Darden, T. A.; Duke, R. E.; Ghoreishi, D.; Gilson,
M. K.; Gohlke, H.; Goetz, A. W.; Greene, D.; Harris, R.; Homeyer, N.; Izadi, S.;
Kovalenko, A.; Kurtzman, T.; Lee, T. S.; LeGrand, S.; Li, P.; Lin, C.; Liu, J.;
Luchko, T.; Luo, R.; Mermelstein, D. J.; Merz, K. M.; Miao, Y.; Monard, G.;
Nguyen, C.; Nguyen, H.; Omelyan, I.; Onufriev, A.; Pan, F.; Qi, R.; Roe, D. R.;
Roitberg, A.; Sagui, C.; Schott-Verdugo, S.; Shen, J.; Simmerling, C. L.; Smith,
J.; Salomon-Ferrer, R.; Swails, J.; Walker, R. C.; Wang, J.; Wei, H.; Wolf, R.
M.; Wu, X.; Xiao, L. et al.
AMBER 2018 , 2018.
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.
Huang YD, Chen W, and Shen J*,
Continuous constant pH molecular dynamics with particle-mesh Ewald and
titratable water.
J Chem Theory Comput 12: 5411-5421, 2016.
Chen W, Morrow BH, Shi C, and Shen JK*,
Recent development and application of constant pH molecular dynamics.
Mol Simulat 40: 830-838, 2014.
Nguyen, H.; Roe, D. R.; Simmerling, C.
Improved Generalized Born Solvent Model Parameters for Protein Simulations.
J. Chem. Theory Comput. 2013, 9, 2020−2034.
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.
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.
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.
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.
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.
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.
Wallace JA and Shen JK*,
Predicting protein pKa ’s with continuous constant pH molecular dynamics.
Methods Enzymol 66: 455-475, 2009.
Khandogin J and Brooks CL III*,
Toward the accurate first-principles prediction of ionization equilibria in
proteins.
Biochemistry 45: 9363-9373, 2006.
Khandogin J* and Brooks CL III,
Constant pH molecular dynamics simulation with proton tautomerism.
Biophys J 89: 141-157, 2005.