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Faculty Bio

We conduct research in the field of computational biochemistry and biophysics, focusing on the development and application of computational methods to understand the structure, dynamics, and thermodynamics of important biochemical processes such as protein-ligand and protein-protein interactions, DNA-ligand recognition, and conformational dynamics of proteins and nucleic acids. Our research is supported by active grants from NIH.
See our publications at the Google Scholar Website: https://scholar.google.com/citations?user=OSlOL1gAAAAJ&hl=en

PhD, University of Manchester, Manchester, England, 1995
Physical Chemistry of Macromolecules

BS, Nanjing University, Nanjing, China, 1990
Physics, Acoustics

Past Courses

BIO 395: Independent Study in Biology
BIO 480: Research in Biology
BMB 640: Physical Biochemistry
BMB 710: Research I
BMB 711: Research II
CHE 111: General Chemistry I
CHE 112: General Chemistry II
CHE 335: Mlclr Mdlng & Mchn Lrn Drg Dsc
CHE 340: Polymer Chemistry
CHE 480: Research in Chemistry
CHE 492: Chemistry Seminar II
FOR 500: Introduction to Physical Chem
PHY 101: College Physics I
PHY 102: College Physics II
PHY 111: General Physics I
PHY 112: General Physics II

Publications

Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge
Azimi, S., Wu, J. Z., Khuttan, S., Kurtzman, T., Deng, N. & Gallicchio, E. (2022). Journal of Computer-Aided Molecular Design. Vol 36 (Issue 1) , pages 63-76.

Computational design of small molecular modulators of protein--protein interactions with a novel thermodynamic cycle: Allosteric inhibitors of HIV-1 integrase
Sun, Q., Ramaswamy, V. S., Levy, R. & Deng, N. (2021). Protein Science. Vol 30 (Issue 2) , pages 438--447.

Evaluating Molecular Docking Software for Small Molecule Binding to G-Quadruplex DNA
Dickerhoff, J., Warnecke, K. R., Wang, K., Deng, N. & Yang, D. (2021). International Journal of Molecular Sciences. Vol 22 (Issue 19) , pages 10801.

Alchemical Transfer Approach to Absolute Binding Free Energy Estimation
Wu, J. Z., Azimi, S., Khuttan, S., Deng, N. & Gallicchio, E. (2021). Journal of Chemical Theory and Computation. Vol 17 (Issue 6) , pages 3309-3319.

Molecular Dynamics Free Energy Simulations Reveal the Mechanism for the Antiviral Resistance of the M66I HIV-1 Capsid Mutation
Sun, Q., Levy, R. M., Kirby, K. A., Wang, Z., Sarafianos, S. G. & Deng, N. (2021). Viruses. Vol 13 (Issue 5) , pages 920.

Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory
Chen, L., Cruz, A., Roe, D. R., Simmonett, A., Wickstrom, L., Deng, N. & Kurtzman, T. (2021). Journal of Chemical Theory and Computation.

Exploring the Free Energy Landscape and Thermodynamics of Protein-Protein Association: HIV-1 Integrase Multimerization Induced by an Allosteric Inhibitor
Tse, C., Wickstrom, L., Kvaratskhelia, M., Gallicchio, E., Levy, R. & Deng, N. (2020). Biophysical Journal. Vol 119 (Issue 6) , pages 1226-1238.

Combining Alchemical Transformation with a Physical Pathway to Accelerate Absolute Binding Free Energy Calculations of Charged Ligands to Enclosed Binding Sites
Cruz, J., Wickstrom, L., Yang, D., Gallicchio, E. & Deng, N. (2020). Journal of Chemical Theory and Computation. Vol 16 (Issue 4) , pages 2803-2813.

Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses
Sakae, Y., Zhang, B. W., Levy, R. M. & Deng, N. (2020). Journal of Computational Chemistry. Vol 41 (Issue 1) , pages 56-68.

Ligand Selectivity in the Recognition of Protoberberine Alkaloids by Hybrid-2 Human Telomeric G-Quadruplex: Binding Free Energy Calculation, Fluorescence Binding, and NMR Experiments
Deng, N., Xia, J., Wickstrom, L., Lin, C., Wang, K., He, P., Yin, Y. & Yang, D. (2019). Molecules. Vol 24 (Issue 8) , pages 1574.

Comparing alchemical and physical pathway methods for computing the absolute binding free energy of charged ligands
Deng, N., Cui, D., Zhang, B. W., Xia, J., Cruz, J. & Levy, R. (2018). Physical Chemistry Chemical Physics. Vol 20 (Issue 25) , pages 17081-17092.

Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points
Harris, R. C., Deng, N., Levy, R. M., Ishizuka, R. & Matubayasi, N. (2017). Journal of Computational Chemistry. Vol 38 (Issue 15) , pages 1198-1208.

Binding energy distribution analysis method: Hamiltonian replica exchange with torsional flattening for binding mode prediction and binding free energy estimation
Mentes, A., Deng, N., Vijayan, R., Xia, J., Gallicchio, E. & Levy, R. M. (2016). Journal of Chemical Theory and Computation. Vol 12 (Issue 5) , pages 2459--2470.