2023
Pharmacophore Variants of the Macrocyclic Peptide Triazole Inactivator of HIV-1 Env Journal Article
In: Medicinal Chemistry Research, vol. 32, pp. 1497-1509, 2023.
Piperidine CD4-mimetic compounds expose vulnerable Env epitopes sensitizing HIV-1-infected cells to ADCC Journal Article
In: Viruses, vol. 15, no. 5, pp. 1185, 2023.
Molecular Dynamics Simulations of Ion Permeation in Human Voltage-Gated Sodium Channels Journal Article
In: Journal of Chemical Theory and Computation, vol. 19, iss. 10, pp. 2953–2972, 2023.
Indoline CD4-mimetic Compounds Mediate Potent and Broad HIV-1 Inhibition and Sensitization to Antibody-dependent Cellular Cytotoxicity Journal Article
In: Proceedings of the National Academy of Sciences, vol. 120, pp. e2222073120, 2023.
HTPolyNet: A general system generator for all-atom molecular simulations of amorphous crosslinked polymers Journal Article
In: SoftwareX, vol. 21, pp. 101303, 2023.
2022
Entropic overcompensation of the N501Y mutation on SARS-CoV-2 S binding to ACE2 Journal Article
In: Journal of Chemical Information and Modeling, vol. 63, pp. 633-642, 2022.
Structural and Functional Characterization of Indane-Core CD4-Mimetic Compounds Substituted with Heterocyclic Amines Journal Article
In: ACS Medicinal Chemistry Letters, vol. 14, pp. 51-58, 2022.
VE607 Stabilizes SARS-CoV-2 Spike In the RBD-up Conformation and Inhibits Viral Entry Journal Article
In: iScience, vol. 25, pp. 104528, 2022, ISSN: 2589-0042.
In: Computational Materials Science, vol. 27, pp. 111264, 2022.
Modeling Sizing Emulsion Droplet Deposition onto Silica Using All-Atom Molecular Dynamics Simulations Journal Article
In: Composites Part B: Engineering, vol. 235, pp. 109712, 2022.
2021
Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking Journal Article
In: Journal of Computer Aided Molecular Design, vol. 26, pp. 1-13, 2021.
Identification and Validation of gp120 Residue His105 as a Novel Target for HIV-1
Neutralization by Small-Molecule CD4-Mimics Journal Article
In: ACS Medicinal Chemistry Letters, vol. 12, pp. 1824-1831, 2021.
Atomistic Simulation of Volumetric Properties of Epoxy Networks: Effect of Monomer Length Journal Article
In: Soft Matter, vol. 17, pp. 9957-9986, 2021.
Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2 Journal Article
In: Journal of Biological Chemistry, vol. 297, no. 4, pp. 11051, 2021.
The Roles of Coupling Agent and Surfactant in Droplet Structure in Sizing Emulsions: A Molecular Dynamics Simulations Study Journal Article
In: Langmuir, vol. 37, no. 33, pp. 10183-10190, 2021.
Peptide Triazole Thiol Irreversibly Inactivates Metastable HIV-1 Env by Accessing Conformational Triggers Intrinsic to Virus–Cell Entry Journal Article
In: Microorganisms, vol. 9, no. 6, 2021, ISSN: 2076-2607.
Optimizing String Method’s Reproducibility Using Generalized Solute Tempering Replica Exchange Journal Article
In: The Journal of Physical Chemistry B, vol. 125, no. 24, pp. 6609-6616, 2021.
HIV-1 Env-Dependent Cell Killing by Bifunctional Small-Molecule/Peptide Conjugates Journal Article
In: ACS Chemical Biology, vol. 16, no. 1, pp. 193-204, 2021.
2020
In: Biochemical Journal, vol. 477, no. 21, pp. 4263–4280, 2020, ISSN: 0264-6021.
The HIV-1 Env gp120 Inner Domain Shapes the Phe43 Cavity and the CD4 Binding Site Journal Article
In: mBio, vol. 11, no. 3, pp. e00280-20, 2020.
Long-Acting BMS-378806 Analogues Stabilize the State-1 Conformation of the Human Immunodeficiency Virus Type 1 Envelope Glycoproteins Journal Article
In: Journal of Virology, vol. 94, no. 10, pp. e00148–20, 2020.
Interaction of human ACE2 to membrane-bound SARS-CoV-1 and SARS-CoV-2 S glycoproteins Journal Article
In: Viruses, vol. 12, no. 10, pp. 1104, 2020.
Roles of Variable Linker Length in Dual Acting Virucidal Entry Inhibitors on HIV-1 Potency via On-the-fly Free Energy Molecular Simulations Journal Article
In: Protein Science, vol. 29, pp. 2304-2310, 2020.
Metastable HIV-1 Surface Protein Env Sensitizes Cell Membranes to Transformation and Poration by Dual-Acting Virucidal Entry Inhibitors Journal Article
In: Biochemistry, vol. 59, no. 6, pp. 818–828, 2020.
2019
Optimization of Small Molecules That Sensitize HIV-1 Infected Cells to Antibody-Dependent Cellular Cytotoxicity Journal Article
In: ACS Medicinal Chemistry Letters, vol. 11, no. 3, pp. 371–378, 2019.
Free energy calculation using space filled design and weighted reconstruction: A modified single sweep approach Journal Article
In: Molecular Simulation, vol. 46, no. 3, pp. 193–206, 2019.
Effect of molecular packing and hydrogen bonding on the properties of epoxy-amido amine systems Journal Article
In: Computational Materials Science, vol. 169, pp. 109082, 2019.
Energetics of Flap Opening in HIV-1 Protease: String Method Calculations Journal Article
In: The Journal of Physical Chemistry B, vol. 123, no. 45, pp. 9584–9591, 2019.
In: Journal of Virology, vol. 93, no. 24, pp. e01325–19, 2019.
Mapping saddles and minima on free energy surfaces using multiple climbing strings Journal Article
In: The Journal of Chemical Physics, vol. 151, no. 12, pp. 124112, 2019.
Strain-Dependent Activation and Inhibition of Human Immunodeficiency Virus Entry by a Specific PF-68742 Stereoisomer Journal Article
In: Journal of Virology, vol. 93, no. 21, 2019.
In: Macromolecular Theory and Simulations, vol. 28, no. 6, pp. 1900030, 2019.
Associating HIV-1 envelope glycoprotein structures with states on the~virus observed by smFRET Journal Article
In: Nature, vol. 568, no. 7752, pp. 415–419, 2019.
Yield and Post-yield Behavior of Fatty-Acid-Functionalized Amidoamine–Epoxy Systems: A Molecular Simulation Study Journal Article
In: Journal of Dynamic Behavior of Materials, vol. 5, no. 2, pp. 143–149, 2019.
2018
Counterion Effects on Aggregate Structure of 12-Hydroxystearate Salts in Hexane: A Quantum Mechanical and Molecular Dynamics Simulation Study Journal Article
In: The Journal of Physical Chemistry B, vol. 123, no. 2, pp. 534–541, 2018.
Lipid flip-flop vs. lateral diffusion in the relaxation of hemifusion diaphragms Journal Article
In: Biochimica et Biophysica Acta (BBA) - Biomembranes, vol. 1860, no. 7, pp. 1452–1459, 2018.
The effect of alkyl chain length on mechanical properties of fatty-acid-functionalized amidoamine-epoxy systems Journal Article
In: Computational Materials Science, vol. 150, pp. 70–76, 2018.
In: Proteins: Structure, Function, and Bioinformatics, vol. 86, no. 7, pp. 707–711, 2018.
Effect of Intercalated Water on Potassium Ion Transport through Kv1.2 Channels Studied via On-the-Fly Free-Energy Parametrization Journal Article
In: Journal of Chemical Theory and Computation, vol. 14, no. 5, pp. 2743–2750, 2018.
Testing Convergence of Different Free-Energy Methods in a Simple Analytical System with Hidden Barriers Journal Article
In: Computation, vol. 6, no. 2, pp. 27, 2018.
Restricted HIV-1 Env glycan engagement by lectin-reengineered DAVEI protein chimera is sufficient for lytic inactivation of the virus Journal Article
In: Biochemical Journal, vol. 475, no. 5, pp. 931–957, 2018.
In: ChemMedChem, vol. 13, no. 6, pp. 627–633, 2018.
2017
Rate of hemifusion diaphragm dissipation and ability to form three-junction bound HD determined by lipid composition Journal Article
In: The Journal of Chemical Physics, vol. 147, no. 13, pp. 134903, 2017.
The β20-β21 of gp120 is a regulatory switch for HIV-1 Env conformational transitions Journal Article
In: Nature Communications, vol. 8, no. 1, 2017.
Effects of Optical Purity and Finite System Size on Self-Assembly of 12-Hydroxystearic Acid in Hexane: Molecular Dynamics Simulations Journal Article
In: The Journal of Physical Chemistry B, vol. 121, no. 39, pp. 9223–9233, 2017.
The effect of alkyl chain length on material properties of fatty-acid-functionalized amidoamine-epoxy systems Journal Article
In: European Polymer Journal, vol. 89, pp. 1–12, 2017.
Recognition of HIV-inactivating peptide triazoles by the recombinant soluble Env trimer, BG505 SOSIP.664 Journal Article
In: Proteins: Structure, Function, and Bioinformatics, vol. 85, no. 5, pp. 843–851, 2017.
Polymorphism at 129 dictates metastable conformations of the human prion protein N-terminal β-sheet Journal Article
In: Chemical Science, vol. 8, no. 2, pp. 1225–1232, 2017.
2016
Relationships between molecular structure and thermomechanical properties of bio-based thermosetting polymers Journal Article
In: Journal of Polymer Science Part B: Polymer Physics, vol. 55, no. 3, pp. 285–292, 2016.
Lytic Inactivation of Human Immunodeficiency Virus by Dual Engagement of gp120 and gp41 Domains in the Virus Env Protein Trimer Journal Article
In: Biochemistry, vol. 55, no. 44, pp. 6100–6114, 2016.