Publications by Type: Journal Article

2012
T. S. Kaoud, Yan, C., Mitra, S., Tseng, C. - C., Jose, J., Taliaferro, J. M., Tuohetahuntila, M., Devkota, A., Sammons, R., Park, J., and others,From in silico discovery to intracellular activity: targeting JNK–protein interactions with small molecules,” ACS medicinal chemistry letters, vol. 3, pp. 721–725, 2012.
J. Zhang, Shi, Y., and Ren, P., “Polarizable force fields for scoring protein–ligand interactions,” Protein-Ligand Interactions, First Edition, pp. 99–120, 2012.
X. Mu, Eckes, K. M., Nguyen, M. M., Suggs, L. J., and Ren, P., “Experimental and computational studies reveal an alternative supramolecular structure for Fmoc-dipeptide self-assembly,” Biomacromolecules, vol. 13, pp. 3562–3571, 2012.
T. S. Kaoud, Park, H., Mitra, S., Yan, C., Tseng, C. - C., Shi, Y., Jose, J., Taliaferro, J. M., Lee, K., Ren, P., and others,Manipulating JNK signaling with (-)-zuonin A,” ACS chemical biology, vol. 7, pp. 1873–1883, 2012.
J. Zhang, Yang, W., Piquemal, J. - P., and Ren, P., “Modeling structural coordination and ligand binding in zinc proteins with a polarizable potential,” Journal of chemical theory and computation, vol. 8, pp. 1314–1324, 2012.
R. Xiong, Cai, X. - M., Wei, J., and Ren, P. - Y., “Some insights into the binding mechanism of Aurora B kinase gained by molecular dynamics simulation,” Journal of molecular modeling, vol. 18, pp. 4591–4601, 2012.
P. Ren, Chun, J., Thomas, D. G., Schnieders, M. J., Marucho, M., Zhang, J., and Baker, N. A., “Biomolecular electrostatics and solvation: a computational perspective,” Quarterly reviews of biophysics, vol. 45, pp. 427–491, 2012.
M. J. Schnieders, Kaoud, T. S., Yan, C., Dalby, K. N., and Ren, P., “Computational insights for the discovery of non-ATP competitive inhibitors of MAP kinases,” Current pharmaceutical design, vol. 18, pp. 1173–1185, 2012.
M. J. Schnieders, Baltrusaitis, J., Shi, Y., Chattree, G., Zheng, L., Yang, W., and Ren, P., “The structure, thermodynamics, and solubility of organic crystals from simulation with a polarizable force field,” Journal of chemical theory and computation, vol. 8, pp. 1721–1736, 2012.
J. C. Wu, Chattree, G., and Ren, P., “Automation of AMOEBA polarizable force field parameterization for small molecules,” Theoretical chemistry accounts, vol. 131, pp. 1138, 2012.
Y. Shi, Zhu, C. Z., Martin, S. F., and Ren, P., “Probing the effect of conformational constraint on phosphorylated ligand binding to an SH2 domain using polarizable force field simulations,” The Journal of Physical Chemistry B, vol. 116, pp. 1716–1727, 2012.
A. Marjolin, Gourlaouen, C., Clavaguéra, C., Ren, P. Y., Wu, J. C., Gresh, N., Dognon, J. - P., and Piquemal, J. - P., “Toward accurate solvation dynamics of lanthanides and actinides in water using polarizable force fields: from gas-phase energetics to hydration free energies,” Theoretical Chemistry Accounts, vol. 131, pp. 1198, 2012.
2011
S. Lee, Warthaka, M., Yan, C., Kaoud, T. S., Ren, P., and Dalby, K. N., “Examining docking interactions on ERK2 with modular peptide substrates,” Biochemistry, vol. 50, pp. 9500–9510, 2011.
D. R. Kryscio, Shi, Y., Ren, P., and Peppas, N. A., “Molecular docking simulations for macromolecularly imprinted polymers,” Industrial & engineering chemistry research, vol. 50, pp. 13877–13884, 2011.
D. P. Gardner, Ren, P., Ozer, S., and Gutell, R. R., “Statistical potentials for hairpin and internal loops improve the accuracy of the predicted RNA structure,” Journal of molecular biology, vol. 413, pp. 473–483, 2011.
J. Wu, Zhen, X., Shen, H., Li, G., and Ren, P., “Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent,” The Journal of chemical physics, vol. 135, pp. 10B617, 2011.
P. Ren, Wu, C., and Ponder, J. W., “Polarizable atomic multipole-based molecular mechanics for organic molecules,” Journal of chemical theory and computation, vol. 7, pp. 3143–3161, 2011.
Y. Shi, Wu, C., Ponder, J. W., and Ren, P., “Multipole electrostatics in hydration free energy calculations,” Journal of computational chemistry, vol. 32, pp. 967–977, 2011.
T. Yang, Wu, J. C., Yan, C., Wang, Y., Luo, R., Gonzales, M. B., Dalby, K. N., and Ren, P., “Virtual screening using molecular simulations,” Proteins: Structure, Function, and Bioinformatics, vol. 79, pp. 1940–1951, 2011.
A. Piserchio, Warthaka, M., Devkota, A. K., Kaoud, T. S., Lee, S., Abramczyk, O., Ren, P., Dalby, K. N., and Ghose, R., “Solution NMR insights into docking interactions involving inactive ERK2,” Biochemistry, vol. 50, pp. 3660–3672, 2011.

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