Publications by Year: 2013

2013
T. Fu, Ren, H., Zhang, J., Ren, P., Enyedy, I., and Li, G., “Role of Bivalent Cations in Structural Stabilities of New Drug Targets—Vacciniarelated Kinases (VRK) from Molecular Dynamics Simulations,” Current pharmaceutical design, vol. 19, pp. 2269–2281, 2013.
L. - P. Wang, Head-Gordon, T., Ponder, J. W., Ren, P., Chodera, J. D., Eastman, P. K., Martinez, T. J., and Pande, V. S., “Systematic improvement of a classical molecular model of water,” The Journal of Physical Chemistry B, vol. 117, pp. 9956–9972, 2013.
Y. Shi, Xia, Z., Zhang, J., Best, R., Wu, C., Ponder, J. W., and Ren, P., “Polarizable atomic multipole-based AMOEBA force field for proteins,” Journal of chemical theory and computation, vol. 9, pp. 4046–4063, 2013.
Z. Xia, Huynh, T., Ren, P., and Zhou, R., “Correction: 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, 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.
A. G. Cisneros, Karttunen, M., Ren, P., and Sagui, C., “Classical electrostatics for biomolecular simulations,” Chemical reviews, vol. 114, pp. 779–814, 2013.
S. D. Fried, Wang, L. - P., Boxer, S. G., Ren, P., and Pande, V. S., “Calculations of the electric fields in liquid solutions,” The Journal of Physical Chemistry B, vol. 117, pp. 16236–16248, 2013.
Z. Xia, Bell, D. R., Shi, Y., and Ren, P., “RNA 3D structure prediction by using a coarse-grained model and experimental data,” The Journal of Physical Chemistry B, vol. 117, pp. 3135–3144, 2013.
X. Wu, Shi, Y., Ren, P., Wang, D., and Li, G., “Exploring the Relationship between Sequences, Structures, Dynamical Behaviors and Functions of New Type Protein Drugs: DARPins,” Current pharmaceutical design, vol. 19, pp. 2308–2317, 2013.
Z. Xia and Ren, P., “Prediction and coarse-grained modeling of RNA structures,” in Biophysics of RNA Folding, Springer, New York, NY, 2013, pp. 53–68.
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.