Publications by Type: Journal Article

2011
D. R. Kryscio, Shi, Y., Ren, P., Peppas, N. A., Solov’ev, V. P., Oprisiu, I., Marcou, G., Varnek, A., Seredych, M., Rawlins, J., and others,INFONA-science communication portal,” Industrial & Engineering Chemistry Research, vol. 50, pp. 13877–13884, 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.
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.
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.
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.
2010
J. W. Ponder, Wu, C., Ren, P., Pande, V. S., Chodera, J. D., Schnieders, M. J., Haque, I., Mobley, D. L., and Lambrecht, D. S., “R. a. DiStasio, M. Head-Gordon, GNI Clark, ME Johnson and T. Head-Gordon,” J. Phys. Chem. B, vol. 114, pp. 2549–2564, 2010.
J. Zhang, King, C. A., Dalby, K., and Ren, P., “Conformational preference of ChaK1 binding peptides: a molecular dynamics study,” PMC biophysics, vol. 3, pp. 2, 2010.
J. M. Fonner, Schmidt, C. E., and Ren, P., “A combined molecular dynamics and experimental study of doped polypyrrole,” Polymer, vol. 51, pp. 4985–4993, 2010.
K. Callaway, Waas, W. F., Rainey, M. A., Ren, P., and Dalby, K. N., “Phosphorylation of the transcription factor Ets-1 by ERK2: rapid dissociation of ADP and phospho-Ets-1,” Biochemistry, vol. 49, pp. 3619–3630, 2010.
Z. Xia, Gardner, D. P., Gutell, R. R., and Ren, P., “Coarse-grained model for simulation of RNA three-dimensional structures,” The Journal of Physical Chemistry B, vol. 114, pp. 13497–13506, 2010.
C. Yan, Pattani, V., Tunnell, J. W., and Ren, P., “Temperature-induced unfolding of epidermal growth factor (EGF): insight from molecular dynamics simulation,” Journal of Molecular Graphics and Modelling, vol. 29, pp. 2–12, 2010.
J. C. Wu, Piquemal, J. - P., Chaudret, R., Reinhardt, P., and Ren, P., “Polarizable molecular dynamics simulation of Zn (II) in water using the AMOEBA force field,” Journal of chemical theory and computation, vol. 6, pp. 2059–2070, 2010.
J. W. Ponder, Wu, C., Ren, P., Pande, V. S., Chodera, J. D., Schnieders, M. J., Haque, I., Mobley, D. L., Lambrecht, D. S., DiStasio Jr, R. A., and others,Current status of the AMOEBA polarizable force field,” The journal of physical chemistry B, vol. 114, pp. 2549–2564, 2010.

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