Publications

2013
D. R. Bell, Xia, Z., and Ren, P., “Multiscale modeling of RNA 3D structures,” Biomedical Sciences and Engineering Conference (BSEC), 2013. IEEE, pp. 1-4, 2013.
D. W. Dykstra, Dalby, K. N., and Ren, P., “Elucidating binding modes of zuonin A enantiomers to JNK1 via in silico methods,” Journal of Molecular Graphics and Modelling, vol. 45, pp. 38-44, 2013.
Z. Xia, Huynh, T., Ren, P., and Zhou, R., “Large Domain Motions in Ago Protein Controlled by the Guide DNA-Strand Seed Region Determine the Ago-DNA-mRNA Complex Recognition Process,” PloS one, vol. 8, pp. e54620, 2013.
2012
H. Shen, Xia, Z., Li, G., and Ren, P., “A Review of Physics-Based Coarse-Grained Potentials for the Simulations of Protein Structure and Dynamics,” in Annual Reports in Computational Chemistry, vol. 8, Elsevier, 2012, pp. 129–148.
Z. Xia, Clark, P., Huynh, T., Loher, P., Zhao, Y., Chen, H. - W., Ren, P., Rigoutsos, I., and Zhou, R., “ERRATUM: Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible'seed-less' targets,” Scientific reports, vol. 2, 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.
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.
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, 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.
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.
J. Zhang, Shi, Y., and Ren, P., “Polarizable force fields for scoring protein–ligand interactions,” Protein-Ligand Interactions, First Edition, pp. 99–120, 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.
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.
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.
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.
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.
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.

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