Publications by Type: Journal Article

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.
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.
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.
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. 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.
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.
M. M. Nguyen, Abdelmelek, M., Zhang, J., Ren, P., and Suggs, L. J., “DEVELOPING DEPSIPEPTIDES AS BIOMIMETIC STRUCTURES THROUGH SECONDARY STRUCTURE,” Polymer Preprints, vol. 51, pp. 440, 2010.
2009
D. Jiao, Zhang, J., Duke, R. E., Li, G., Schnieders, M. J., and Ren, P., “Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential,” Journal of computational chemistry, vol. 30, pp. 1701–1711, 2009.
J. C. Wu, Gardner, D. P., Ozer, S., Gutell, R. R., and Ren, P., “Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding,” Journal of molecular biology, vol. 391, pp. 769–783, 2009.
2008
H. - X. Li, Hwang, B. - Y., Laxmikanthan, G., Blaber, S. I., Blaber, M., Golubkov, P. A., Ren, P., Iverson, B. L., and Georgiou, G., “Substrate specificity of human kallikreins 1 and 6 determined by phage display,” Protein Science, vol. 17, pp. 664–672, 2008.
P. A. Golubkov, Wu, J. C., and Ren, P., “A transferable coarse-grained model for hydrogen-bonding liquids,” Physical chemistry chemical Physics, vol. 10, pp. 2050–2057, 2008.
D. Jiao, Golubkov, P. A., Darden, T. A., and Ren, P., “Calculation of protein–ligand binding free energy by using a polarizable potential,” Proceedings of the National Academy of Sciences, vol. 105, pp. 6290–6295, 2008.
P. A. Golubkov, Wu, J. C., and Ren, P., “A transferable coarse-grained model for hydrogen-bonding liquids,” Physical Chemistry Chemical Physics, vol. 10, pp. 2050-2057, 2008.
D. Jiao, Golubkov, P. A., Darden, T. A., and Ren, P., “Calculation of protein–ligand binding free energy by using a polarizable potential,” Proceedings of the National Academy of Sciences, vol. 105, pp. 6290-6295, 2008.
H. - X. Li, Hwang, B. - Y., Laxmikanthan, G., Blaber, S. I., Blaber, M., Golubkov, P. A., Ren, P., Iverson, B. L., and Georgiou, G., “Substrate specificity of human kallikreins 1 and 6 determined by phage display,” Protein Science, vol. 17, pp. 664-672, 2008.
2007
M. J. Schnieders, Baker, N. A., Ren, P., and Ponder, J. W., “Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum,” The Journal of chemical physics, vol. 126, pp. 03B623, 2007.

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