Publications by Type: Journal Article

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
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.
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.
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.
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
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.

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