Publications

134 entries « 1 of 3 »

2023

Monisha Gupta; Gabriela Canziani; Charles G. Ang; Mohammadjavad Mohammadi; Cameron F. Abrams; Derek Yang; Amos B. Smith, III; Irwin Chaiken

Pharmacophore Variants of the Macrocyclic Peptide Triazole Inactivator of HIV-1 Env Journal Article

In: Medicinal Chemistry Research, vol. 32, pp. 1497-1509, 2023.

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Shilei Ding; William D. Tolbert; Huile Zhu; Daniel Lee; Tyler Higgins; Xuchen Zhao; Dung Nguyen; Rebekah Sherburn; Jonathan Richard; Gabrielle-Gendron Lepage; Halima Medjahed; Mohammadjavad Mohammadi; Cameron Abrams; Marzena Pazgier; Amos B. Smith III; Andrés Finzi

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.

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Giulio Alberini; Sergio Alexis Paz; Beatrice Corradi; Cameron Abrams; Fabio Benfenati; Luca Maragliano

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.

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Christopher Fritcshi; Saumya Anang; Zhen Gong; Mohammadjavad Mohammadi; Jonathan Richard; Catherine Bourassa; Kenny T. Severino; Hannah Richter; Derek Yang; Hung-Ching Chen; Ta-Jung Chiu; Michael S. Seaman; Navid Madani; Cameron F. Abrams; Andrès Finzi; Wayne A. Hendrickson; Joseph Sodroski; Amos B. Smith III

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.

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Ming Huang; Cameron F. Abrams

HTPolyNet: A general system generator for all-atom molecular simulations of amorphous crosslinked polymers Journal Article

In: SoftwareX, vol. 21, pp. 101303, 2023.

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2022

Natasha Gupta Vergara; Megan Gatchel; Cameron F. Abrams

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.

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Cheyenne Chaplain; Christopher J. Fritschi; Saumya Anang; Zhen Gong; Jonathan Richard; Catherine Bourassa; Shuaiyi Liang; Mohammadjavad Mohammadi; Jun Park; Andrés Finzi; Navid Madani; Joseph G. Sodroski; Cameron F. Abrams; Wayne A. Hendrickson; Amos B. Smith III

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.

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Shilei Ding; Irfan Ullah; Shang Yu Gong; Jonathan Grover; Mohammadjavad Mohammadi; Yaozong Chen; Dani Vézina; Guillaume Beaudoin-Bussi`eres; Vijay Tailor Verma; Guillaume Goyette; Fleur Gaudette; Jonathan Richard; Derek Yang; A. Smith III; Marzena Pazgier; Marceline C^oté; Cameron Abrams; Priti Kumar; Walther Mothes; Pradeep Uchil; Andrés Finzi; Christian Baron

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.

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Ming Huang; Nicolas Alvarez; Giuseppe Palmese; Cameron F. Abrams

The Effect of Network Topology on Material Properties in Vinyl-ester/Styrene Thermoset Polymers using Molecular Dynamics Simulations and Time-Temperature Superposition Journal Article

In: Computational Materials Science, vol. 27, pp. 111264, 2022.

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Salman Zarrini; Cameron F. Abrams

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.

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2021

Sergio Ribone; Sergio Alexis Paz; Cameron Abrams; Marcos Villarreal

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.

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Christopher Fritschi; Shuaiyi Liang; Mohammadjavad Mohammadi; Saumya Anang; Francesca Moraca; Junhua Chen; Navid Madani; Joseph Sodroski; Cameron Abrams; Wayne Hendrickson; Amos B. Smith III

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.

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Ketan Khare; Cameron F. Abrams

Atomistic Simulation of Volumetric Properties of Epoxy Networks: Effect of Monomer Length Journal Article

In: Soft Matter, vol. 17, pp. 9957-9986, 2021.

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Jérémie Prévost; Jonathan Richard; Romain Gasser; Shilei Ding; Clément Fage; Sai Priya Anand; Damien Adam; Natasha Gupta Vergara; Alexandra Tauzin; Mehdi Benlarbi; Shang Yu Gong; Guillaume Goyette; Anik Privé; Sandrine Moreira; Hugues Charest; Michel Roger; Walther Mothes; Marzena Pazgier; Emmanuelle Brochiero; Guy Boivin; Cameron F Abrams; Arne Schön; Andrés Finzi

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.

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Salman Zarrini; Cameron F. Abrams

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.

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Charles Gotuaco Ang; Erik Carter; Ann Haftl; Shiyu Zhang; Adel A. Rashad; Michele Kutzler; Cameron F. Abrams; Irwin M. Chaiken

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.

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Gourav Shrivastav; Cameron F. Abrams

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.

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Althea Gaffney; Aakansha Nangarlia; Charles G. Ang; Steven Gossert; Adel Ahmed Rashad Ahmed; Md Alamgir Hossain; Cameron F. Abrams; Amos B. Smith III; Irwin Chaiken

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.

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2020

Bibek Parajuli; Kriti Acharya; Aakansha Nangarlia; Shiyu Zhang; Bijay Parajuli; Alexej Dick; Brendon Ngo; Cameron F. Abrams; Irwin Chaiken

Identification of a glycan cluster in gp120 essential for irreversible HIV-1 lytic inactivation by a lectin-based recombinantly engineered protein conjugate Journal Article

In: Biochemical Journal, vol. 477, no. 21, pp. 4263–4280, 2020, ISSN: 0264-6021.

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Jérémie Prévost; William D. Tolbert; Halima Medjahed; Rebekah T. Sherburn; Navid Madani; Daria Zoubchenok; Gabrielle Gendron-Lepage; Althea E. Gaffney; Melissa C. Grenier; Sharon Kirk; Natasha Vergara; Changze Han; Brendan T. Mann; Agnès L. Chénine; Adel Ahmed; Irwin Chaiken; Frank Kirchhoff; Beatrice H. Hahn; Hillel Haim; Cameron F. Abrams; Amos B. Smith III; Joseph Sodroski; Marzena Pazgier; Andrés Finzi

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.

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Shitao Zou; Shijian Zhang; Althea Gaffney; Haitao Ding; Maolin Lu; Jonathan R. Grover; Mark Farrell; Hanh T. Nguyen; Connie Zhao; Saumya Anang; Meiqing Zhao; Mohammadjavad Mohammadi; Scott C. Blanchard; Cameron Abrams; Navid Madani; Walther Mothes; John C. Kappes; Amos B. Smith III; Joseph Sodroski

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.

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Sai Priya Anand; Yaozong Chen; Jérémie Prévost; Romain Gasser; Guillaume Beaudoin-Bussiéres; Cameron F. Abrams; Marzena Pazgier; Andrés Finzi

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.

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Steven Gossert; Bibek Parajuli; Irwin Chaiken; Cameron F. Abrams

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.

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Charles G. Ang; Md. Alamgir Hossain; Marg Rajpara; Harry Bach; Kriti Acharya; Alexej Dick; Adel A. Rashad; Michele Kutzler; Cameron F. Abrams; Irwin Chaiken

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.

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2019

Melissa C. Grenier; Shilei Ding; Dani Vézina; Jean-Philippe Chapleau; William D. Tolbert; Rebekah Sherburn; Arne Schön; Sambasivarao Somisetti; Cameron F. Abrams; Marzena Pazgier; Andrés Finzi; Amos B. Smith III

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.

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Anindya Bhaduri; Jasmine Gardner; Cameron F. Abrams; Lori Graham-Brady

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.

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Arun Srikanth Sridhar; Cameron F. Abrams

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.

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Jasmine M. Gardner; Cameron F. Abrams

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.

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Shilei Ding; Melissa C. Grenier; William D. Tolbert; Dani Vézina; Rebekah Sherburn; Jonathan Richard; Jérémie Prévost; Jean-Philippe Chapleau; Gabrielle Gendron-Lepage; Halima Medjahed; Cameron Abrams; Joseph Sodroski; Marzena Pazgier; Amos B. Smith III; Andrés Finzi

A New Family of Small-Molecule CD4-Mimetic Compounds Contacts Highly Conserved Aspartic Acid 368 of HIV-1 gp120 and Mediates Antibody-Dependent Cellular Cytotoxicity Journal Article

In: Journal of Virology, vol. 93, no. 24, pp. e01325–19, 2019.

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Gourav Shrivastav; Eric Vanden-Eijnden; Cameron F. Abrams

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.

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Connie Zhao; Amy M. Princiotto; Hanh T. Nguyen; Shitao Zou; Meiqing Lily Zhao; Shijian Zhang; Alon Herschhorn; Mark Farrell; Karanbir Pahil; Bruno Melillo; Somisetti V. Sambasivarao; Cameron Abrams; Amos B. Smith III; Navid Madani; Joseph Sodroski

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.

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Ming Huang; Cameron Abrams

Effects of Reactivity Ratios on Network Topology and Thermomechanical Properties in Vinyl Ester/Styrene Thermosets: Molecular Dynamics Simulations Journal Article

In: Macromolecular Theory and Simulations, vol. 28, no. 6, pp. 1900030, 2019.

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Maolin Lu; Xiaochu Ma; Luis R. Castillo-Menendez; Jason Gorman; Nirmin Alsahafi; Utz Ermel; Daniel S. Terry; Michael Chambers; Dongjun Peng; Baoshan Zhang; Tongqing Zhou; Nick Reichard; Kevin Wang; Jonathan R. Grover; Brennan P. Carman; Matthew R. Gardner; Ivana Nikić-Spiegel; Akihiro Sugawara; James Arthos; Edward A. Lemke; Amos B. Smith III; Michael Farzan; Cameron Abrams; James B. Munro; Adrian B. McDermott; Andrés Finzi; Peter D. Kwong; Scott C. Blanchard; Joseph G. Sodroski; Walther Mothes

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.

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Arun Srikanth Sridhar; C. F. Abrams

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.

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2018

Ryan Gordon; Spencer T. Stober; Cameron F. Abrams

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.

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Jasmine M. Gardner; Cameron F. Abrams

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.

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Arun Srikanth Sridhar; Emre Kinaci; John Vergara; Giuseppe Palmese; Cameron F. Abrams

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.

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Steven T. Gossert; Bibek Parajuli; Irwin Chaiken; Cameron F. Abrams

Roles of conserved tryptophans in trimerization of HIV-1 membrane-proximal external regions: Implications for virucidal design via alchemical free-energy molecular simulations Journal Article

In: Proteins: Structure, Function, and Bioinformatics, vol. 86, no. 7, pp. 707–711, 2018.

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S. Alexis Paz; Luca Maragliano; Cameron F. Abrams

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.

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S. Paz; Cameron Abrams

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.

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Bibek Parajuli; Kriti Acharya; Harry C. Bach; Bijay Parajuli; Shiyu Zhang; Amos B. Smith III; Cameron F. Abrams; Irwin Chaiken

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.

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Francesca Moraca; David Rinaldo; Amos B. Smith III; Cameron F. Abrams

Specific Noncovalent Interactions Determine Optimal Structure of a Buried Ligand Moiety: QM/MM and Pure QM Modeling of Complexes of the Small-Molecule CD4 Mimetics and HIV-1 gp120 Journal Article

In: ChemMedChem, vol. 13, no. 6, pp. 627–633, 2018.

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2017

Jasmine M. Gardner; Cameron F. Abrams

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.

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Alon Herschhorn; Christopher Gu; Francesca Moraca; Xiaochu Ma; Mark Farrell; Amos B. Smith III; Marie Pancera; Peter D. Kwong; Arne Schön; Ernesto Freire; Cameron Abrams; Scott C. Blanchard; Walther Mothes; Joseph G. Sodroski

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.

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Ryan Gordon; Spencer T. Stober; Cameron F. Abrams

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.

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Arun Srikanth Sridhar; John Vergara; Giuseppe Palmese; Cameron F. Abrams

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.

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Kriti Acharya; Adel A. Rashad; Francesca Moraca; Per Johan Klasse; John P. Moore; Cameron Abrams; Irwin Chaiken

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.

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S. Alexis Paz; Eric Vanden-Eijnden; Cameron F. Abrams

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.

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2016

Jung Ho Yang; Arun Srikanth; Changwoon Jang; Cameron F. Abrams

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.

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Bibek Parajuli; Kriti Acharya; Reina Yu; Brendon Ngo; Adel A. Rashad; Cameron F. Abrams; Irwin M. Chaiken

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.

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134 entries « 1 of 3 »