Publications by Year: 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.
C. Yan, Kaoud, T., Lee, S., Dalby, K. N., and Ren, P., “Understanding the specificity of a docking interaction between JNK1 and the scaffolding protein JIP1,” The Journal of Physical Chemistry B, vol. 115, pp. 1491–1502, 2011.
S. Lee, Warthaka, M., Yan, C., Kaoud, T. S., Piserchio, A., Ghose, R., Ren, P., and Dalby, K. N., “A model of a MAPK• substrate complex in an active conformation: A computational and experimental approach,” PLoS One, vol. 6, pp. e18594, 2011.