N. Deng

发表

Parameterization of an effective potential for protein–ligand binding from host–guest affinity data

M. Gilson, R. Levy, E. Gallicchio, 2016, Journal of molecular recognition : JMR.

Resolving the Ligand-Binding Specificity in c-MYC G-Quadruplex DNA: Absolute Binding Free Energy Calculations and SPR Experiment.

P. Cieplak, Danzhou Yang, L. Wickstrom, 2017, The journal of physical chemistry. B.

Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory

Andrew C. Simmonett, D. Roe, L. Wickstrom, 2020 .

HIV-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors

A. Engelman, R. Levy, D. Lyumkis, 2019, eLife.

Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.

Bin W. Zhang, R. Levy, N. Deng, 2015, Journal of chemical theory and computation.

Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening Against the Flap Site of HIV Protease

Arthur J. Olson, Lauren Wickstrom, Stefano Forli, 2014, The journal of physical chemistry. B.

Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory.

Andrew C. Simmonett, D. Roe, L. Wickstrom, 2020, Journal of chemical theory and computation.

Alchemical Transfer Approach to Absolute Binding Free Energy Estimation.

E. Gallicchio, N. Deng, S. Azimi, 2021, Journal of chemical theory and computation.

DFT Study on the Reactive Species of Metalloporphyrin Catalytic Oxidation

Luhai Li, L. Mo, Meijuan Cao, 2020 .

Exploring the Free-Energy Landscape and Thermodynamics of Protein-Protein Association.

R. Levy, E. Gallicchio, L. Wickstrom, 2020, Biophysical journal.

Mechanisms of HIV-1 Integrase Resistance to Dolutegravir and Potent Inhibition of Drug Resistant Variants

S. Hughes, Steven J Smith, A. Haldane, 2022, bioRxiv.

Computational design of small molecular modulators of protein–protein interactions with a novel thermodynamic cycle: Allosteric inhibitors of HIV‐1 integrase

R. Levy, R. Vijayan, N. Deng, 2020, Protein science : a publication of the Protein Society.

Mechanisms of HIV-1 Integrase Resistance to Dolutegravir and Potent Inhibition of Drug Resistant Variants

S. Hughes, Steven J Smith, A. Haldane, 2023, bioRxiv.

Indenoisoquinoline Topoisomerase Inhibitors Strongly Bind and Stabilize the MYC Promoter G-Quadruplex and Downregulate MYC.

Danzhou Yang, M. Cushman, M. S. Elsayed, 2019, Journal of the American Chemical Society.

The mechanism of H171T resistance reveals the importance of Nδ-protonated His171 for the binding of allosteric inhibitor BI-D to HIV-1 integrase

A. Engelman, R. Levy, E. Poeschla, 2014, Retrovirology.

The mechanism of H171T resistance reveals the importance of Nδ-protonated His171 for the binding of allosteric inhibitor BI-D to HIV-1 integrase

A. Engelman, R. Levy, E. Poeschla, 2014, Retrovirology.

Ligand Selectivity in the Recognition of Protoberberine Alkaloids by Hybrid-2 Human Telomeric G-Quadruplex: Binding Free Energy Calculation, Fluorescence Binding, and NMR Experiments

Danzhou Yang, L. Wickstrom, J. Xia, 2019, Molecules.

Molecular Dynamics Free Energy Simulations Reveal the Mechanism for the Antiviral Resistance of the M66I HIV-1 Capsid Mutation

R. Levy, S. Sarafianos, N. Deng, 2021, Viruses.

Developing end-point methods for absolute binding free energy calculation using the Boltzmann-quasiharmonic model.

E. Gallicchio, L. Wickstrom, Lieyang Chen, 2022, Physical chemistry chemical physics : PCCP.

Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations.

Michael Andrec, Emilio Gallicchio, Ronald M Levy, 2011, The journal of physical chemistry. B.

Using Molecular Dynamics Free Energy Simulation to Compute Binding Affinities of DNA G-Quadruplex Ligands.

N. Deng, 2019, Methods in molecular biology.

Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid

A. Olson, S. Sarafianos, R. Vijayan, 2022, Journal of Computer-Aided Molecular Design.

A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core Domain*

A. Engelman, Erik Serrao, R. Levy, 2016, The Journal of Biological Chemistry.

Allosteric HIV‐1 integrase inhibitors promote aberrant protein multimerization by directly mediating inter‐subunit interactions: Structural and thermodynamic modeling studies

A. Engelman, R. Levy, M. Kvaratskhelia, 2016, Protein science : a publication of the Protein Society.

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

Nobuyuki Matubayasi, Ryosuke Ishizuka, Ronald M. Levy, 2017, J. Comput. Chem..

Evaluating Molecular Docking Software for Small Molecule Binding to G-Quadruplex DNA

Danzhou Yang, N. Deng, J. Dickerhoff, 2021, International journal of molecular sciences.

Exploring the Free Energy Landscape and Thermodynamics of Protein-Protein Association: HIV-1 Integrase Multimerization Induced by an Allosteric Inhibitor

R. Levy, L. Wickstrom, M. Kvaratskhelia, 2020, bioRxiv.

Combining Alchemical Transformation with Physical Pathway to Accelerate Absolute Binding Free Energy Calculations of Charged Ligands to Enclosed Binding Sites.

E. Gallicchio, Danzhou Yang, L. Wickstrom, 2020, Journal of chemical theory and computation.

HIV-1 Integrase Tetramers are the Antiviral Target of Pyridine-based Allosteric Integrase 1 Inhibitors 2 3

A. Engelman, R. Levy, D. Lyumkis, 2022 .

Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge

N. Deng, S. Azimi, T. Kurtzman, 2021, Journal of Computer-Aided Molecular Design.

Comparing alchemical and physical pathway methods for computing the absolute binding free energy of charged ligands.

Bin W Zhang, Junchao Xia, Bin W. Zhang, 2018, Physical chemistry chemical physics : PCCP.

Indenoisoquinoline Topoisomerase Inhibitors Strongly Bind and Stabilize the MYC Promoter G-Quadruplex and Downregulate MYC.

Danzhou Yang, M. Cushman, M. S. Elsayed, 2019, Journal of the American Chemical Society.