Publications by authors named "Ronald Levy"

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Predicting side chain conformations in folded proteins by AlphaFold: Perspective and challenges.
Gia G Maisuradze, Abhishek Thakur, Kisan Khatri, Allan Haldane, Ronald M Levy

Biophys J· November 2025

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mRNA Delivery to the Lung Vascular Endothelium by Dicationic Charge-Altering Releasable Transporters.
Mahmoud M AbdElwakil, Jeffrey Ni, Summer Ramsay-Burrough, Paul Joshua Hurst, Rebecca L McClellan, Ronald Levy

J Am Chem Soc· November 2025

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Using phage display for rational engineering of a higher-affinity humanized 3' phosphohistidine-specific antibody.
Gregory D Martyn, Rajasree Kalagiri, Gianluca Veggiani, Robyn L Stanfield, Indrani Choudhuri, Ronald M Levy

Commun Chem· November 2025

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Benchmarking Free Energy Calculations: Analysis of Single and Double Mutations Across Two Simulation Software Platforms for Two Protein Systems.
Shivani Gupta, Qinfang Sun, Ronald M Levy

bioRxiv· October 2025

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Co-occurrence of clonally related follicular lymphoma and histiocytic sarcoma.
Sarah Haebe, Debra K Czerwinski, Anuja Sathe, Susan M Grimes, Tianqi Chen, Ronald Levy

Blood Cancer J· August 2025

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Development of an in situ CAR-T cell protocol through optical and PSMA-targeted PET imaging.
Nisi Zhang, Jai Woong Seo, Elise Robinson, Angelie Rivera-Rodriguez, James Wang, Ronald Levy

Proc Natl Acad Sci U S A· June 2025

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Evolutionary Sequence and Structural Basis for the Epistatic Origins of Drug Resistance in HIV.
Avik Biswas, Indrani Choudhuri, Kenneth Huang, Qinfang Sun, Andrej Sali, Ronald M Levy

bioRxiv· May 2025

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De Novo Hydration of Cryo-EM Reconstructions through Molecular Dynamics Simulations of the Excess Chemical Potential.
Qinfang Sun, Sriram Aiyer, Avik Biswas, Allan Haldane, Sompriya Chatterjee, Ronald M Levy

bioRxiv· May 2025

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A Phase I Clinical Trial Adding OX40 Agonism to In Situ Therapeutic Cancer Vaccination in Patients with Low-Grade B-cell Lymphoma Highlights Challenges in Translation from Mouse to Human Studies.
Tanaya Shree, Debra Czerwinski, Sarah Haebe, Anuja Sathe, Sue Grimes, Ronald Levy

Clin Cancer Res· March 2025

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Phylogenetic Corrections and Higher-Order Sequence Statistics in Protein Families: The Potts Model vs MSA Transformer.
Kisan Khatri, Ronald M Levy, Allan Haldane

ArXiv· March 2025

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Using AlphaFold2 to Predict the Conformations of Side Chains in Folded Proteins.
Gia G Maisuradze, Abhishek Thakur, Kisan Khatri, Allan Haldane, Ronald M Levy

bioRxiv· February 2025

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Entrenchment and contingency in neutral protein evolution with epistasis.
Lisa Schmelkin, Vincenzo Carnevale, Allan Haldane, Jeffrey P Townsend, Sarah Chung, Ronald M Levy

bioRxiv· January 2025

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Using phage display for rational engineering of a higher affinity humanized 3' phosphohistidine-specific antibody.
Gregory D Martyn, Rajasree Kalagiri, Gianluca Veggiani, Robyn L Stanfield, Indrani Choudhuri, Ronald M Levy

bioRxiv· November 2024

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Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases.
Joan Gizzio, Abhishek Thakur, Allan Haldane, Carol Beth Post, Ronald M Levy

Nat Commun· August 2024

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Isoprenoid CARTs: and mRNA Delivery by Charge-Altering Releasable Transporters Functionalized with Archaea-inspired Branched Lipids.
Harrison P Rahn, Jiuzhi Sun, Zhijian Li, Robert M Waymouth, Ronald Levy

Biomacromolecules· July 2024

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Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases.
Joan Gizzio, Abhishek Thakur, Allan Haldane, Carol Beth Post, Ronald M Levy

bioRxiv· May 2024

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Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases.
Joan Gizzio, Abhishek Thakur, Allan Haldane, Ronald M Levy

Res Sq· May 2024

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Kinetic coevolutionary models predict the temporal emergence of HIV-1 resistance mutations under drug selection pressure.
Avik Biswas, Indrani Choudhuri, Eddy Arnold, Dmitry Lyumkis, Allan Haldane, Ronald M Levy

Proc Natl Acad Sci U S A· April 2024

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Potts Hamiltonian Models and Molecular Dynamics Free Energy Simulations for Predicting the Impact of Mutations on Protein Kinase Stability.
Abhishek Thakur, Joan Gizzio, Ronald M Levy

J Phys Chem B· February 2024

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A clinical trial of therapeutic vaccination in lymphoma with serial tumor sampling and single-cell analysis.
Tanaya Shree, Sarah Haebe, Debra K Czerwinski, Erik Eckhert, Grady Day, Ronald Levy

Blood Adv· January 2024

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Elucidating the Molecular Determinants of the Binding Modes of a Third-Generation HIV-1 Integrase Strand Transfer Inhibitor: The Importance of Side Chain and Solvent Reorganization.
Qinfang Sun, Avik Biswas, Dmitry Lyumkis, Ronald Levy, Nanjie Deng

Viruses· January 2024

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Follicular lymphoma evolves with a surmountable dependency on acquired glycosylation motifs in the B-cell receptor.
Sarah Haebe, Grady Day, Debra K Czerwinski, Anuja Sathe, Susan M Grimes, Ronald Levy

Blood· December 2023

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Elucidating the molecular determinants for binding modes of a third-generation HIV-1 integrase strand transfer inhibitor: Importance of side chain and solvent reorganization.
Qinfang Sun, Avik Biswas, Dmitry Lyumkis, Ronald Levy, Nanjie Deng

bioRxiv· December 2023

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Single-cell multi-gene identification of somatic mutations and gene rearrangements in cancer.
Susan M Grimes, Heon Seok Kim, Sharmili Roy, Anuja Sathe, Carlos I Ayala, Ronald Levy

NAR Cancer· September 2023

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Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants.
Min Li, Dario Oliveira Passos, Zelin Shan, Steven J Smith, Qinfang Sun, Ronald M Levy

Sci Adv· July 2023

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