Publications by Type: Journal Article

2014
M. Warthaka, Adelmann, C. H., Kaoud, T. S., Edupuganti, R., Yan, C., Johnson Jr, W. H., Ferguson, S., Tavares, C. D., Pence, L. J., Anslyn, E. V., and others,Quantification of a pharmacodynamic ERK end point in melanoma cell lysates: toward personalized precision medicine,” ACS medicinal chemistry letters, vol. 6, pp. 47–52, 2014.
H. Shen, Li, Y., Ren, P., Zhang, D., and Li, G., “Anisotropic coarse-grained model for proteins based on Gay–Berne and electric multipole potentials,” Journal of chemical theory and computation, vol. 10, pp. 731–750, 2014.
X. Mu, Wang, Q., Wang, L. - P., Fried, S. D., Piquemal, J. - P., Dalby, K. N., and Ren, P., “Modeling organochlorine compounds and the $\sigma$-hole effect using a polarizable multipole force field,” The Journal of Physical Chemistry B, vol. 118, pp. 6456–6465, 2014.
F. Lipparini, Lagardère, L., Stamm, B., Cancès, E., Schnieders, M., Ren, P., Maday, Y., and Piquemal, J. - P., “Scalable evaluation of polarization energy and associated forces in polarizable molecular dynamics: I. toward massively parallel direct space computations,” Journal of Chemical Theory and Computation, vol. 10, pp. 1638–1651, 2014.
Q. Wang, Park, J., Devkota, A. K., Cho, E. J., Dalby, K. N., and Ren, P., “Identification and validation of novel PERK inhibitors,” Journal of chemical information and modeling, vol. 54, pp. 1467–1475, 2014.
K. M. Eckes, Mu, X., Ruehle, M. A., Ren, P., and Suggs, L. J., “$\beta$ Sheets not required: Combined experimental and computational studies of self-assembly and gelation of the ester-containing analogue of an Fmoc-dipeptide hydrogelator,” Langmuir, vol. 30, pp. 5287–5296, 2014.
J. R. Abella, Cheng, S. Y., Wang, Q., Yang, W., and Ren, P., “Hydration free energy from orthogonal space random walk and polarizable force field,” Journal of chemical theory and computation, vol. 10, pp. 2792–2801, 2014.
R. Edupuganti, Wang, Q., Tavares, C. D. J., Chitjian, C. A., Bachman, J. L., Ren, P., Anslyn, E. V., and Dalby, K. N., “Synthesis and biological evaluation of pyrido [2, 3-d] pyrimidine-2, 4-dione derivatives as eEF-2K inhibitors,” Bioorganic & medicinal chemistry, vol. 22, pp. 4910–4916, 2014.
Z. Xia, Wang, Q., Mu, X., and Ren, P., “Development of AMOEBA Force Field with Advanced Electrostatics,” Molecular Modeling at the Atomic Scale: Methods and Applications in Quantitative Biology, pp. 83, 2014.
C. D. J. Tavares, Ferguson, S. B., Giles, D. H., Wang, Q., Wellmann, R. M., O'Brien, J. P., Warthaka, M., Brodbelt, J. S., Ren, P., and Dalby, K. N., “

The Molecular Mechanism of Eukaryotic Elongation Factor 2 Kinase Activation

,” Journal of Biological Chemistry, vol. 289, pp. 23901-23916 (PMCID: PMC4156036), 2014.
H. Shen, Li, Y., Ren, P., Zhang, D., and Li, G., “An Anisotropic Coarse-Grained Model for Proteins Based On Gay-Berne and Electric Multipole Potentials,” Journal of Chemical Theory and Computation, vol. 10, pp. 731–750, 2014.
A. G. Cisneros, Karttunen, M., Ren, P., and Sagui, C., “Classical Electrostatics for Biomolecular Simulations,” Chemical reviews, vol. 114, pp. 779–814, 2014.
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,” 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.
A. G. Cisneros, Karttunen, M., Ren, P., and Sagui, C., “Classical electrostatics for biomolecular simulations,” Chemical reviews, vol. 114, pp. 779–814, 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.
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.

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