Ronald M. Levy

Also affiliated with Institute of Molecular Biology and Biophysics, Temple University

Biochemistry, Genetics and Molecular BiologyPhysics and AstronomyMaterials ScienceImmunology and MicrobiologyMedicine

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 32 papers. Top paper: “Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants”.

Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants

Science Advances(2023)10.1126/sciadv.adg5953

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0.843DataRank · unranked

38 citations

Dario Oliveira Passos, Zelin Shan, Steven J. Smith, Qinfang Sun, Avik Biswas +14 more

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

Viruses(2021)10.3390/v13050920

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0.442DataRank · unranked

18 citations

Ronald M. Levy, Karen A. Kirby, Zhengqiang Wang, Stefan G. Sarafianos, Nanjie Deng +1 more

Contingency and Entrenchment of Drug-Resistance Mutations in HIV Viral Proteins

The Journal of Physical Chemistry B(2022)10.1021/acs.jpcb.2c06123

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0.385DataRank · unranked

12 citations

Avik Biswas, Allan Haldane, Ronald M. Levy, Indrani Choudhuri

Evolutionary Sequence and Structural Basis for the Epistatic Origins of Drug Resistance in HIV

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.04.30.651576

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0.165DataRank · unranked

2 citations

Indrani Choudhuri, Kenneth Huang, Qinfang Sun, Andrej Săli, Ignacia Echeverria +4 more

Cavity Particle in Aqueous Solution with a Hydrophobic Solute: Structure, Energetics, and Functionals

The Journal of Physical Chemistry B(2020)10.1021/acs.jpcb.0c02721

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0DataRank · unranked

2 citations

Nobuyuki Matubayasi, Ronald M. Levy, Bin W. Zhang

Insights into the energy landscapes of chromosome organization proteins from coevolutionary sequence variation and structural modeling

Proceedings of the National Academy of Sciences(2020)10.1073/pnas.1921727117

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0DataRank · unranked

2 citations

Ronald M. Levy

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.29.177592

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0DataRank · unranked

1 citations

Lauren Wickstrom, Mamuka Kvaratskhelia, Emilio Gallicchio, Ronald M. Levy, Nan Deng +1 more

The generative capacity of probabilistic protein sequence models

Nature Communications(2021)10.1038/s41467-021-26529-9

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0DataRank · unranked

42 citations

Sandro Hauri, Quentin Novinger, Slobodan Vučetić, Ronald M. Levy, Vincenzo Carnevale +2 more

Protein Loop Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates

The Journal of Physical Chemistry Letters(2021)10.1021/acs.jpclett.1c00778

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0DataRank · unranked

8 citations

Bin W. Zhang, Ronald M. Levy, Shima Arasteh

The role of epistasis in determining the fitness landscape of HIV proteins

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.16.448646

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0DataRank · unranked

1 citations

Allan Haldane, Ronald M. Levy, Avik Biswas

Unique Features of Different Classes of G-Protein-Coupled Receptors Revealed from Sequence Coevolutionary and Structural Analysis

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.03.446974

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0DataRank · unranked

0 citations

Allan Haldane, Ronald M. Levy, Yinglong Miao, N. Hung

Evolutionary divergence in the conformational landscapes of tyrosine vs serine/threonine kinases

eLife(2022)10.7554/elife.83368

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0DataRank · unranked

35 citations

Abhishek Thakur, Allan Haldane, Ronald M. Levy, Joan Gizzio

Limits to detecting epistasis in the fitness landscape of HIV

PLoS ONE(2022)10.1371/journal.pone.0262314

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0DataRank · unranked

11 citations

Allan Haldane, Ronald M. Levy, Avik Biswas

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

Journal of Computer-Aided Molecular Design(2022)10.1007/s10822-022-00446-5

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0DataRank · unranked

8 citations

Avik Biswas, R. S. K. Vijayan, Pierrick Craveur, Stefano Forli, Arthur J. Olson +6 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.04.519057

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0DataRank · unranked

3 citations

Dario Oliveira Passos, Zelin Shan, Steven J. Smith, Qinfang Sun, Avik Biswas +12 more

Kinetic co-evolutionary models predict the temporal emergence of HIV resistance mutations under drug selection pressure

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.30.518575

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0DataRank · unranked

1 citations

Indrani Choudhuri, Eddy Arnold, Dmitry Lyumkis, Allan Haldane, Ronald M. Levy +1 more

Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases

Nature Communications(2024)10.1038/s41467-024-50812-0

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0DataRank · unranked

23 citations

Abhishek Thakur, Allan Haldane, Carol Beth Post, Ronald M. Levy, Joan Gizzio

Kinetic coevolutionary models predict the temporal emergence of HIV-1 resistance mutations under drug selection pressure

Proceedings of the National Academy of Sciences(2024)10.1073/pnas.2316662121

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0DataRank · unranked

18 citations

Indrani Choudhuri, Eddy Arnold, Dmitry Lyumkis, Allan Haldane, Ronald M. Levy +1 more

Potts Hamiltonian Models and Molecular Dynamics Free Energy Simulations for Predicting the Impact of Mutations on Protein Kinase Stability

The Journal of Physical Chemistry B(2024)10.1021/acs.jpcb.3c08097

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0DataRank · unranked

13 citations

Joan Gizzio, Ronald M. Levy, Abhishek Thakur

Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.08.584161

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0DataRank · unranked

6 citations

Abhishek Thakur, Allan Haldane, Carol Beth Post, Ronald M. Levy, Joan Gizzio

Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases

Research square(2024)10.21203/rs.3.rs-4048991/v1

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0DataRank · unranked

1 citations

Joan Gizzio, Abhishek Thakur, Allan Haldane, Ronald M. Levy

Using phage display for rational engineering of a higher affinity humanized 3’phosphohistidine-specific antibody

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.11.04.621849

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0DataRank · unranked

1 citations

Rajasree Kalagiri, Gianluca Veggiani, Robyn L. Stanfield, Indrani Choudhuri, Margaux Sala +9 more

Phylogenetic corrections and higher-order sequence statistics in protein families: Potts vs multiple sequence alignment transformer machine learning models

Physical Review Research(2025)10.1103/g5cx-1vhj

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0DataRank · unranked

3 citations

Ronald M. Levy, Allan Haldane, Kisan Khatri

Predicting side chain conformations in folded proteins by AlphaFold: Perspective and challenges

Biophysical Journal(2025)10.1016/j.bpj.2025.09.030

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0DataRank · unranked

2 citations

Abhishek Thakur, Kumar Khatri, Allan Haldane, Ronald M. Levy, Gia G. Maisuradze

Using AlphaFold2 to Predict the Conformations of Side Chains in Folded Proteins

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.02.10.637534

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0DataRank · unranked

1 citations

Abhishek Thakur, Kumar Khatri, Allan Haldane, Ronald M. Levy, Gia G. Maisuradze

De Novo Hydration of Cryo-EM Reconstructions through Molecular Dynamics Simulations of the Excess Chemical Potential

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.23.655847

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0DataRank · unranked

0 citations

Sriram Aiyer, Avik Biswas, Allan Haldane, Sompriya Chatterjee, Nobuyuki Matubayasi +3 more

Benchmarking Free Energy Calculations: Analysis of Single and Double Mutations Across Two Simulation Software Platforms for Two Protein Systems

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.10.19.683321

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0DataRank · unranked

0 citations

Qichu Sun, Ronald M. Levy, Shivani Gupta

Mi3-GPU: MCMC-based inverse Ising inference on GPUs for protein covariation analysis

Computer Physics Communications(2020)10.1016/j.cpc.2020.107312

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0DataRank · unranked

47 citations

Ronald M. Levy, Allan Haldane

Using phage display for rational engineering of a higher-affinity humanized 3’ phosphohistidine-specific antibody

Communications Chemistry(2025)10.1038/s42004-025-01768-9

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0DataRank · unranked

0 citations

Rajasree Kalagiri, Gianluca Veggiani, Robyn L. Stanfield, Indrani Choudhuri, Margaux Sala +9 more

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

Biophysical Journal(2020)10.1016/j.bpj.2020.08.005

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0DataRank · unranked

28 citations

Lauren Wickstrom, Mamuka Kvaratskhelia, Emilio Gallicchio, Ronald M. Levy, Nanjie Deng +1 more

Solvation Thermodynamics from the Perspective of Endpoints DFT

The Journal of Physical Chemistry B(2020)10.1021/acs.jpcb.0c08988

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0DataRank · unranked

6 citations

Nobuyuki Matubayasi, Bin W. Zhang, Ronald M. Levy

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

Protein Science(2020)10.1002/pro.4004

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0DataRank · unranked

8 citations

Vijayan S. K. Ramaswamy, Ronald M. Levy, Nanjie Deng, Qinfang Sun