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.
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.