Publications by Year: 2017

2017
Z. Jing, Liu, C., Cheng, S., Qi, R., Walker, B., Piquemal, J. - P., and Ren, P., “Polarizable force fields for biomolecular simulations: Recent advances and applications,” annual review of biophysics, 2017.
S. Deng, Wang, Q., and Ren, P., “Estimating and modeling charge transfer from the SAPT induction energy,” Journal of computational chemistry, vol. 38, pp. 2222–2231, 2017.
X. Han, Jing, Z., Wu, W., Zou, B., Peng, Z., Ren, P., Wikramanayake, A., Lu, Z., and Leblanc, R. M., “Biocompatible and blood–brain barrier permeable carbon dots for inhibition of A$\beta$ fibrillation and toxicity, and BACE1 activity,” Nanoscale, vol. 9, pp. 12862–12866, 2017.
C. Zhang, Bell, D., Harger, M., and Ren, P., “Polarizable Multipole-Based Force Field for Aromatic Molecules and Nucleobases,” Journal of chemical theory and computation, vol. 13, pp. 666–678, 2017.
R. Edupuganti, Taliaferro, J. M., Wang, Q., Xie, X., Cho, E. J., Vidhu, F., Ren, P., Anslyn, E. V., Bartholomeusz, C., and Dalby, K. N., “Discovery of a potent inhibitor of MELK that inhibits expression of the anti-apoptotic protein Mcl-1 and TNBC cell growth,” Bioorganic & medicinal chemistry, vol. 25, pp. 2609–2616, 2017.
D. R. Bell, Cheng, S. Y., Salazar, H., and Ren, P., “Capturing RNA folding free energy with coarse-grained molecular dynamics simulations,” Scientific Reports, vol. 7, pp. 45812, 2017.
S. Cheng, Bell, D., and Ren, P., “RACER a Coarse-Grained RNA Model for Capturing Folding Free Energy in Molecular Dynamics Simulations,” in APS Meeting Abstracts, 2017.
J. M. Obliosca, Cheng, S. Y., Chen, Y. - A., Llanos, M. F., Liu, Y. - L., Imphean, D. M., Bell, D. R., Petty, J. T., Ren, P., and Yeh, H. - C., “LNA Thymidine Monomer Enables Differentiation of the Four Single-Nucleotide Variants by Melting Temperature,” Journal of the American Chemical Society, vol. 139, pp. 7110–7116, 2017.
C. Liu, Qi, R., Wang, Q., Piquemal, J. - P., and Ren, P., “Capturing many-body interactions with classical dipole induction models,” Journal of chemical theory and computation, vol. 13, pp. 2751–2761, 2017.
M. Harger, Li, D., Wang, Z., Dalby, K., Lagardère, L., Piquemal, J. - P., Ponder, J., and Ren, P., “Tinker-OpenMM: absolute and relative alchemical free energies using AMOEBA on GPUs,” Journal of computational chemistry, vol. 38, pp. 2047–2055, 2017.
B. S. Wendel, He, C., Qu, M., Wu, D., Hernandez, S. M., Ma, K. - Y., Liu, E. W., Xiao, J., Crompton, P. D., Pierce, S. K., and others,Accurate immune repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children,” Nature communications, vol. 8, pp. 531, 2017.
C. Wang, Ren, P., and Luo, R., “Ionic Solution: What Goes Right and Wrong with Continuum Solvation Modeling,” The Journal of Physical Chemistry B, vol. 121, pp. 11169–11179, 2017.
Z. Jing, Qi, R., Liu, C., and Ren, P., “Study of interactions between metal ions and protein model compounds by energy decomposition analyses and the AMOEBA force field,” The Journal of Chemical Physics, vol. 147, pp. 161733, 2017.
J. A. Rackers, Wang, Q., Liu, C., Piquemal, J. - P., Ren, P., and Ponder, J. W., “An optimized charge penetration model for use with the AMOEBA force field,” Physical Chemistry Chemical Physics, vol. 19, pp. 276–291, 2017.
X. Han, Jing, Z. F., Wu, W., Zou, B., Peng, Z. L., Ren, P. Y., Wikramanayake, A., Lu, Z. M., and Leblanc, R. M., “Biocompatible and blood-brain barrier permeable carbon dots for inhibition of A beta fibrillation and toxicity, and BACE1 activity,” Nanoscale, vol. 9, pp. 12862-12866, 2017.Abstract
Amyloid-beta peptide (A beta) fibrillation is pathologically associated with Alzheimer's disease (AD), and this has resulted in the development of an A beta inhibitor which is essential for the treatment of AD. However, the design of potent agents which can target upstream secretases, inhibit A beta toxicity and aggregation, as well as cross the blood-brain barrier remains challenging. In, this research carbon dots for AD treatment were investigated in vitro using experimental and computational methods for the first time. The results presented here demonstrate a novel strategy for the discovery of novel antiamyloidogenic agents for AD treatments.
S. Deng, Wang, Q., and Ren, P., “Estimating and modeling charge transfer from the SAPT induction energy,” Journal of Computational Chemistry, 2017.
B. S. Wendel, He, C. F., Qu, M. J., Wu, D., Hernandez, S. M., Ma, K. Y., Liu, E. W., Xiao, J., Crompton, P. D., Pierce, S. K., Ren, P. Y., Chen, K. K., and Jiang, N., “Accurate immune repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children,” Nature Communications, vol. 8, 2017.Abstract
Accurately measuring antibody repertoire sequence composition in a small amount of blood is challenging yet important for understanding repertoire responses to infection and vaccination. We develop molecular identifier clustering-based immune repertoire sequencing (MIDCIRS) and use it to study age-related antibody repertoire development and diversification before and during acute malaria in infants (<12 months old) and toddlers (12-47 months old) with 4-8ml of blood. Here, we show this accurate and high-coverage repertoire-sequencing method can use as few as 1000 naive B cells. Unexpectedly, we discover high levels of somatic hypermutation in infants as young as 3 months old. Antibody clonal lineage analysis reveals that somatic hypermutation levels are increased in both infants and toddlers upon infection, and memory B cells isolated from individuals who previously experienced malaria continue to induce somatic hypermutations upon malaria rechallenge. These results highlight the potential of antibody repertoire diversification in infants and toddlers.
C. Liu, Qi, R., Wang, Q., Piquemal, J. - P., and Ren, P., “Capturing Many-Body Interactions with Classical Dipole Induction Models,” Journal of Chemical Theory and Computation, vol. 13, pp. 2751–2761, 2017.
M. Harger, Li, D., Wang, Z., Dalby, K., Lagardere, L., Piquemal, J. P., Ponder, J., and Ren, P. Y., “Tinker-OpenMM: Absolute and Relative Alchemical Free Energies using AMOEBA on GPUs,” Journal of Computational Chemistry, vol. 38, pp. 2047-2055, 2017.Abstract
The capabilities of the polarizable force fields for alchemical free energy calculations have been limited by the high computational cost and complexity of the underlying potential energy functions. In this work, we present a GPU-based general alchemical free energy simulation platform for polarizable potential AMOEBA. Tinker-OpenMM, the OpenMM implementation of the AMOEBA simulation engine has been modified to enable both absolute and relative alchemical simulations on GPUs, which leads to a similar to 200-fold improvement in simulation speed over a single CPU core. We show that free energy values calculated using this platform agree with the results of Tinker simulations for the hydration of organic compounds and binding of host-guest systems within the statistical errors. In addition to absolute binding, we designed a relative alchemical approach for computing relative binding affinities of ligands to the same host, where a special path was applied to avoid numerical instability due to polarization between the different ligands that bind to the same site. This scheme is general and does not require ligands to have similar scaffolds. We show that relative hydration and binding free energy calculated using this approach match those computed from the absolute free energy approach. (C) 2017 Wiley Periodicals, Inc.
R. Edupuganti, Taliaferro, J. M., Wang, Q., Xie, X., Cho, E. J., Vidhu, F., Ren, P., Anslyn, E. V., Bartholomeusz, C., and Dalby, K. N., “Discovery of a potent inhibitor of MELK that inhibits expression of the anti-apoptotic protein Mcl-1 and TNBC cell growth,” Bioorganic & Medicinal Chemistry, vol. 25, no. 9, pp. 2609-2616, 2017.

Pages