Upcoming Publications

• Choudhuri, Indrani; Avik Biswas; Allan Haldane; Ronald M. Levy (2022), Temporal Evolution of the HIV Viral Population under Drug Selection Pressure. BioRxiv DOI: https://doi.org/10.1101/2022.11.30.518575
• Min Li, Dario Oliveira Passos, Zelin Shan, Steven J. Smith, Qinfang Sun, Avik Biswas, Indrani Choudhuri, Timothy S. Strutzenberg, Allan Haldane, Nanjie Deng, Zhaoyang Li, Xue Zhi Zhao, Terrence R. Burke, Jr., Ronald M. Levy, Stephen H. Hughes, Robert Craigie, Dmitry Lyumkis (2022), Mechanisms of HIV-1 Integrase Resistance to Dolutegravir and Potent Inhibition of Drug Resistant Variants. BioRxiv DOI: https://doi.org/10.1101/2022.12.04.519057

Publications

• Gizzo, Joan, Abhishek Thakur, Allan Haldane, Ronald M Levy (2022).Evolutionary divergence in the conformational landscapes of Tyrosine vs Serine/Threonine Kinases eLife , Web publication. DOI:https://doi.org/10.7554/eLife.83368. PMCID: PMC9822262. .
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• Choudhuri, Indrani, Avik Biswas, Allan Haldane, Ronald M. Levy (2022).Contingency and Entrenchment of drug-resistance mutations in HIV viral proteins The Journal of Physical Chemistry B , Web publication. DOI:https://doi.org/10.1021/acs.jpcb.2c06123. PMCID: PMC9841799.
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• Sun, Qinfang, Avik Biswas, R. S. K. Vijayan, Pierrick Craveur, Stefano Forli, Arthur J. Olson, Andres Emanuelli Castaner, Karen A. Kirby, Stefan G. Sarafianos, Nanjie Deng and Ronald Levy (2022).Structure-based Virtual Screening Workflow to Identify Antivirals Targeting HIV-1 Capsid. Journal of Computer-Aided Molecular Design , Web publication. DOI:https://doi.org/10.1007/s10822-022-00446-5. PMCID: PMC8904208.
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• Biswas, Avik, Allan Haldane, and Ronald M. Levy (2022). Limits to detecting epistasis in the fitness landscape of HIV. PLOS ONE, 17(1), e0262314. DOI: https://doi.org/10.1371/journal.pone.0262314. PMCID: PMC8765623.
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• McGee, Francisco, Sandro Hauri, Quentin Novinger, Slobodan Vucetic, Ronald M. Levy, Vincenzo Carnevale, and Allan Haldane (2021). The generative capacity of probabilistic protein sequence models. Nature Communications, 12(1). DOI: https://doi.org/10.1038/s41467-021-26529-9. PMCID: PMC8563988.
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• Do, Hung N., Allan Haldane, Ronald M. Levy, and Yinglong Miao (2021). Unique features of different classes of G-protein-coupled receptors revealed from sequence coevolutionary and structural analysis. Proteins, 1(14). DOI: https://doi.org/10.1002/prot.26256. PMCID:PMC8738117.
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• Sun, Qinfang, Ronald M. Levy, Karen A. Kirby, Zhengqiang Wang, Stefan G. Sarafianos, and Nanjie Deng (2021). Molecular Dynamics Free Energy Simulations Reveal the Mechanism for the Antiviral Resistance of the M66I HIV-1 Capsid Mutation. Viruses, 13(5), 920. DOI: https://doi.org/10.3390/v13050920. PMCID: PMC8156065.
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• Arasteh, Shima, Bin W. Zhang, and Ronald M. Levy (2021). Protein Loop Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates. The Journal of Physical Chemistry Letters, Web publication. DOI: https://doi.org/10.1021/acs.jpclett.1c00778. PMCID: PMC8170697.
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• Levy, Ronald M., Nobuyuki Matubayasi, and Bin W. Zhang (2020). Solvation Thermodynamics from the Perspective of Endpoints {DFT}. The Journal of Physical Chemistry B, 124(52), 11771-11782. DOI: https://dx.doi.org/10.1021/acs.jpcb.0c08988. PMCID: PMC8056868.
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• Sun, Qinfang, R.S.K. Vijayan, Ronald Levy, and Nanjie Deng (2020). Computational Design of Small Molecular Modulators of Protein-Protein Interactions with a Novel Thermodynamic Cycle: Allosteric Inhibitors of {HIV} -1 Integrase. Protein Science, 30(2), 438-447. DOI: https://doi.org/10.1002/pro.4004. PMCID: PMC7784772.
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• Tse, Celine, Lauren Wickstrom, Mamuka Kvaratskhelia, Emilio Gallicchio, Ronald Levy, and Nanjie Deng (2020). Exploring the Free Energy Landscape and Thermodynamics of Protein-Protein Association: {HIV}-1 Integrase Multimerization Induced by an Allosteric Inhibitor. Biophysical Journal, 119, 1226–1238. DOI: https://doi.org/10.1016/j.bpj.2020.08.005. PMCID: PMC7499063.
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• Zhang, Bin W., Nobuyuki Matubayasi, and Ronald M. Levy (2020). Cavity Particle in Aqueous Solution with a Hydrophobic Solute: Structure, Energetics, and Functionals. The Journal of Physical Chemistry B, 124. DOI: 10.1021/acs.jpcb.0c02721. PMCID: PMC8083014.
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• Haldane, Allan and Ronald M. Levy (2020). Mi3-{GPU}: {MCMC}-based inverse Ising inference on {GPUs} for protein covariation analysis. Computer Physics Communications, 260, 107312. DOI: https://doi.org/10.1016/j.cpc.2020.107312. PMCID: PMC7944406.
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• Narayan, Brajesh, Arman Fathizadeh, Clark Templeton, Peng He, Shima Arasteh, Ron Elber, Nicolae-Viorel Buchete, and Ron M. Levy (2020). The transition between active and inactive conformations of Abl kinase studied by rock climbing and Milestoning. Biochimica et Biophysica Acta ({BBA}) - General Subjects, 1864(4), 129508. DOI: 10.1016/j.bbagen.2019.129508. PMCID: PMC7012767.
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• Levy, Ronald M. (2020). Insights into the energy landscapes of chromosome organization proteins from coevolutionary sequence variation and structural modeling. Proceedings of the National Academy of Sciences, 117(5), 201921727. DOI: 10.1073/pnas.1921727117. PMCID: PMC7007567.
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• Cui, Di, Bin W. Zhang, Zhiqiang Tan, and Ronald M. Levy (2019). Ligand Binding Thermodynamic Cycles: Hysteresis, the Locally Weighted Histogram Analysis Method, and the Overlapping States Matrix. Journal of Chemical Theory and Computation, 16(1). DOI: 10.1021/acs.jctc.9b00740. PMCID: PMC7137390.
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• Sakae, Yoshitake, Bin W. Zhang, Ronald M. Levy, and Nanjie Deng (2019). Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses. Journal of Computational Chemistry, 41(1), 56-68. DOI: 10.1002/jcc.26078. PMCID: PMC7140983.
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• Biswas, Avik, Allan Haldane, Eddy Arnold, and Ronald M Levy (2019). Epistasis and entrenchment of drug resistance in {HIV}-1 subtype B. {eLife}, 8. DOI: 10.7554/eLife.50524. PMCID: PMC6783267.
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• Koneru, Pratibha C, Ashwanth C Francis, Nanjie Deng, Stephanie V Rebensburg, Ashley C Hoyte, Jared Lindenberger, Daniel Adu-Ampratwum, Ross C Larue, Michael F Wempe, Alan N Engelman, Dmitry Lyumkis, James R Fuchs, Ronald M Levy, Gregory B Melikyan, and Mamuka Kvaratskhelia (2019). {HIV}-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors. {eLife}, 8. DOI: 10.7554/eLife.46344. PMCID: PMC6581505.
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• Ishii, Yoshiki, Naoki Yamamoto, Nobuyuki Matubayasi, Bin W. Zhang, Di Cui, and Ronald M. Levy (2019). Spatially-Decomposed Free Energy of Solvation Based on the Endpoint Density-Functional Method. Journal of Chemical Theory and Computation, 15(5). DOI: 10.1021/acs.jctc.8b01309. PMCID: PMC6570404.
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• Haldane, Allan and Ronald M. Levy (2019). Influence of multiple-sequence-alignment depth on Potts statistical models of protein covariation. Physical Review E, 99(3). DOI: 10.1103/PhysRevE.99.032405. PMCID: PMC6508952.
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• Xia, Junchao, William Flynn, Emilio Gallicchio, Keith Uplinger, Jonathan D. Armstrong, Stefano Forli, Arthur J. Olson, and Ronald M. Levy (2019). Massive-Scale Binding Free Energy Simulations of {HIV} Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the {IBM} {WCG} Distributed Network. Journal of Chemical Information and Modeling, 59(4), 1382-1397. DOI: 10.1021/acs.jcim.8b00817. PMCID: PMC6496938.
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• Zhang, Bin W., Shima Arasteh, and Ronald M. Levy (2019). The {UWHAM} and {SWHAM} Software Package. Scientific Reports, 9(1). DOI: 10.1038/s41598-019-39420-x. PMCID: PMC6391495.
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• Deng, Nanjie, Di Cui, Bin W. Zhang, Junchao Xia, Jeffrey Cruz, and Ronald M. Levy (2018). Comparing alchemical and physical pathway methods for computing the absolute binding free energy of charged ligands. Journal of Phys. Chem. Chem. Phys., 20(25), 17081-17092. DOI: 10.1039/C8CP01524D. PMCID:PMC6061996.
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• Xia, Junchao, William Flynn, and Ronald M. Levy (2018). Improving Prediction Accuracy of Binding Free Energies and Poses of {HIV} Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials. Journal of Chemical Information and Modeling, 58(7), 1356-1371. DOI: 10.1021/acs.jcim.8b00194. PMCID: PMC6287956.
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• He, Peng, Bin W. Zhang, Shima Arasteh, Lingle Wang, Robert Abel, and Ronald M. Levy (2018). Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates. The Journal of Physical Chemistry Letters, 9(15), 4428-4435. DOI: 10.1021/acs.jpclett.8b01851. PMCID: PMC6092130.
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• Zhang, Bin W., Di Cui, Nobuyuki Matubayasi, and Ronald M. Levy (2018). The Excess Chemical Potential of Water at the Interface with a Protein from End Point Simulations. The Journal of Physical Chemistry B, 122(17), 4700-4707. DOI: 10.1021/acs.jpcb.8b02666. PMCID: PMC5939383.
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• Haldane, Allan, William F. Flynn, Peng He, and Ronald M. Levy (2018). Coevolutionary Landscape of Kinase Family Proteins: Sequence Probabilities and Functional Motifs. Biophysical Journal , 114(1), 21-31. DOI: 10.1016/j.bpj.2017.10.028. PMCID: PMC5773752.
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• Cui, Di, Bin W. Zhang, Nobuyuki Matubayasi, and Ronald M. Levy (2018). The Role of Interfacial Water in Protein–Ligand Binding: Insights from the Indirect Solvent Mediated Potential of Mean Force. Journal of Chemical Theory and Computation, 14(2), 512–526. DOI: 10.1021/acs.jctc.7b01076. PMCID: PMC5897112.
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• Flynn, William F., Allan Haldane, Bruce E. Torbett, and Ronald M. Levy (2017). Inference of epistatic effects leading to entrenchment and drug resistance in HIV-1 protease. Molecular Biology and Evolution, 34(6), 1291. DOI: 10.1093/molbev/msx095. PMCID: PMC5435099.
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• Zhang, Bin W., Nanjie Deng, Zhiqiang Tan, and Ronald M. Levy (2017). Stratified UWHAM and Its Stochastic Approximation for Multicanonical Simulations Which are Far from Equilibrium. Journal of Chemical Theory and Computation, 13(10), 4660-4674. DOI: 10.1021/acs.jctc.7b00651. PMCID: PMC5897113.
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• Levy, Ronald M., Di Cui, Bin W. Zhang, and Nobuyuki Matubayasi (2017). The Relationship Between Solvation Thermodynamics from IST and DFT Perspectives. The Journal of Physical Chemistry B, 121(15), 3825-3841. DOI: 10.1021/acs.jpcb.6b12889. PMCID: PMC5869707.
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• Harris, Robert C., Nanjie Deng, Ronald M. Levy, Ryosuyke Ishizuka, and Nobuyuki Matubayasi (2017). 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. Journal of Computational Chemistry, 38, 1198-1208. DOI: 10.1002/jcc.24668. PMCID: PMC5403615.
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• Levy, Ronald M., Allan Haldane, and William F. Flynn (2017). Potts Hamiltonian models of protein co-variation, free energy landscapes, and evolutionary fitness . Current Opinion in Structural Biology, 43, 55-62. DOI: 10.1016/j.sbi.2016.11.004. PMCID: PMC5869684.
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• Levy, Ronald M. (2016). Recollection. Protein Science, 25, 9-11. DOI: 10.1002/pro.2844. PMCID: PMC4815298.
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• Deng, Nanjie, Ashley Hoyte, Yara E Mansour, Mosaad S. Mohamed, James R. Fuchs, Alan N. Engelman, Mamuka Kvaratskhelia, and Ronald M. Levy (2016). Allosteric HIV-1 integrase inhibitors promote aberrant protein multimerization by directly mediating inter-subunit interactions: Structural and thermodynamic modeling studies. Protein Science, 25(11), 1911-1917. DOI: 10.1002/pro.2997. PMCID: PMC5079246.
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• Pal, Rajat Kumar, Kamran Haider, Divya Kaur, William Flynn Junchao Xia, Ronald M. Levy, Tetiana Taran, Lauren Wickstrom, Tom Kurtzman, and Emilio Gallicchio (2016). A combined treatment of hydration and dynamical effects for the modeling of host--guest binding thermodynamics: the SAMPL5 blinded challenge. Journal of Computer-Aided Molecular Design, Web publication. DOI: 10.1007/s10822-016-9956-6. PMCID: PMC5477994.
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• Deng, Nanjie, William F. FLynn, Junchao Xia, R. S. K. Vijayan, Baofeng Zhang, Peng He, Ahmet Mentes, Emilio Gallicchio, and Ronald M. Levy (2016). Large scale free energy calculations for blind predictions of protein--ligand binding: the D3R Grand Challenge 2015. Journal of Computer-Aided Molecular Design, 30(9), 743-751. DOI: 10.1007/s10822-016-9952-x. PMCID: PMC5869689.
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• Patel, Disha, Janet Antwi, Pratibha C Koneru, Erik Serrao, Stefano Forli, Jacques J Kessl, Lei Feng, Nanjie Deng, Ronald M. Levy, James R. Fuchs, Arthur J. Olson, Alan N. Engelman, Joseph D Bauman, Mamuka Kvaratskhelia, and Eddy Arnold (2016). A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core Domain. Journal of Biological Chemistry, Web publication. DOI: 10.1074/jbc.M116.753384. PMCID: PMC5095411.
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• Haldane, Allan, William F. Flynn, Peng He, R. S. K. Vijayan, and Ronald M. Levy (2016). Structural propensities of kinase family proteins from a Potts model of residue co-variation. Protein Science, 25(8), 1378-1384. DOI: 10.1002/pro.2954. PMCID: PMC4972195.
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• Mentes, Ahmet, Nan-Jie Deng, R. S. K. Vijayan, Junchao Xia, Emilio Gallicchio, and Ronald M. Levy (2016). Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation. Journal of Chemical Theory and Computation, 12(5), 2459-2470. DOI: 10.1021/acs.jctc.6b00134. PMCID: PMC4862910.
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• Zhang, Bin W., Wei Dai, Emilio Gallicchio, Peng He, Junchao Xia, Zhiqiang Tan, and Ronald M. Levy (2016). Simulating Replica Exchange: Markov State Models, Proposal Schemes and the Infinite Swapping Limit. The Journal of Physical Chemistry B, Web publication. DOI: 10.1021/acs.jpcb.6b02015. PMCID: PMC5001888.
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• Tan, Zhiqiang, Junchao Xia, Bin W. Zhang, and Ronald M. levy (2016). Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation. The Journal of Chemical Physics, 144(3). DOI: 10.1063/1.4939768. PMCID: PMC4729400.
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• Zhang, Bin W., Junchao Xia, Zhiqiang Tan, and Ronald M. Levy (2015). A Stochastic Solution to the Unbinned WHAM Equations. Journal of Physical Chemistry Letters, 6, 3834-3840. DOI: 10.1021/acs.jpclett.5b01771. PMCID: PMC4894662.
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• Wickstrom, Lauren, Nanjie Deng, Peng He, Ahmet Mentes, Crystal Nguyen, Michael K. Gilson, Tom Kurtzman, Emilio Gallicchio, and Ronald M. Levy (2015). Parameterization of an effective potential for protein-ligand binding from host-guest affinity data. Journal of Molecular Recognition, 29, 10-21. DOI: 10.1002/jmr.2489. PMCID: PMC4715590.
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• Xia, Junchao, William F. Flynn, Emilio Gallicchio, Bin W. Zhang, Peng He, Zhiqiang Tan, and Ronald M. Levy (2015). Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis. J. Comput. Chem., 36(23), 1772-1785. DOI: 10.1002/jcc.23996. PMCID: PMC4512903.
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• Dai, Wei, Anirvan M. Sengupta, and Ronald M. Levy (2015). First Passage Times, Lifetimes, and Relaxation Times of Unfolded Proteins. Phys. Rev. Lett., 115(4), 048101. DOI: 10.1103/PhysRevLett.115.048101. PMCID: PMC4531052.
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• Deng, Nanjie, Bin W. Zhang, and Ronald M. Levy (2015). Connecting Free Energy Surfaces in Implicit and Explicit Solvent: An Efficient Method To Compute Conformational and Solvation Free Energies. J. Chem. Theory Comput., 11(6), 2868-2878. DOI: 10.1021/acs.jctc.5b00264. PMCID: PMC4521639.
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• Gallicchio, Emilio, Junchao Xia, William F. Flynn, Baofeng Zhang, Sade Samlalsingh, Ahmet Mentes, and Ronald M. Levy (2015). Asynchronous replica exchange software for grid and heterogeneous computing. Computer Physics Communications, Web publication. DOI: 10.1016/j.cpc.2015.06.010. PMCID: PMC4832917
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• Flynn, William F., Max W. Chang, Zhiqiang Tan, Glenn Oliveira, Jinyun Yuan, Jason F. Okulicz, Bruce E. Torbett, and Ronald M. Levy (2015). Deep Sequencing of Protease Inhibitor Resistant HIV Patient Isolates Reveals Patterns of Correlated Mutations in Gag and Protease. PLoS Comput Biol, 11(4), e1004249. DOI: 10.1371/journal.pcbi.1004249. PMCID: PMC4404092.
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• Gallicchio, Emilio, Haoyuan Chen, He Chen, Michael Fitzgerald, Yang Gao, Peng He, Malathi Kalyanikar, Chuan Kao, Beidi Lu, Yijie Niu, Manasi Pethe, Jie Zhu, and Ronald M. Levy (2015). BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge. Journal of Computer-Aided Molecular Design, 29(4), 315-325. DOI: 10.1007/s10822-014-9795-2.
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• Vijayan, R. S. K., Peng He, Vivek Modi, Krisna C. Duong-Ly, Haiching Ma, Jeffrey R. Peterson, Roland L. Dunbrack, and Ronald M. Levy (2015). Conformational Analysis of the DFG-Out Kinase Motif and Biochemical Profiling of Structurally Validated Type II Inhibitors. Journal of Medicinal Chemistry, 58(1), 466-479. DOI: 10.1021/jm501603h. PMCID: PMC4326797.
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• Deng, Nanjie, Stefano Forli, Peng He, Alex Perryman, Lauren Wickstrom, R. S. K. Vijayan, Theresa Tiefenbrunn, David Stout, Emilio Gallicchio, Arthur J. Olson, and Ronald M. Levy (2015). Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening Against the Flap Site of HIV Protease. J. Phys. Chem. B, 119(3), 976-988. DOI: 10.1021/jp506376z. PMCID: PMC4306491.
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• Slaughter, Alison, Kellie A Jurado, Nanjie Deng, Lei Feng, Jacques J Kessl, Nikoloz Shkriabai, Ross C Larue, Hind J Fadel, Pratiq A Patel, Nivedita Jena, James R Fuchs, Eric Poeschla, Ronald M Levy, Alan Engelman, and Mamuka Kvaratskhelia (2014). The mechanism of H171T resistance reveals the importance of Nδ-protonated His171 for the binding of allosteric inhibitor BI-D to HIV-1 integrase. Retrovirology, 11(100). DOI: 10.1186/s12977-014-0100-1. PMCID: PMC4251946.
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• Xia, Junchao and Ronald M. Levy (2014). Molecular Dynamics of the Proline Switch and Its Role in Crk Signaling. J. Phys. Chem. B, 118(17), 4535-4545. DOI: 10.1021/jp5013297. PMCID: PMC4007982.
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• Gallicchio, Emilio, Nanjie Deng, Peng He, Lauren Wickstrom, Alexander L. Perryman, Daniel N. Santiago, Stefano Forli, Arthur J. Olson, and Ronald M. Levy (2014). Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge. Journal of Computer-Aided Molecular Design, 28(4), 475-490. DOI: 10.1007/s10822-014-9711-9. PMCID: PMC4137862.
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• Deng, Nan-jie, Wei Dai, and Ronald M. Levy (2013). How Kinetics within the Unfolded State Affects Protein Folding: An Analysis Based on Markov State Models and an Ultra-Long MD Trajectory. J. Phys. Chem. B, 117(42), 12787-12799. DOI: 10.1021/jp401962k. PMCID: PMC3808496.
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• Yi, Guohua, Mauro Lapelosa, Rachel Bradley, Thomas M. Mariano, Denise Elsasser Dietz, Scott Hughes, Terri Wrin, Chris Petropoulos, Emilio Gallicchio, Ronald M. Levy, Eddy Arnold, and Gail Ferstandig Arnold (2013). Chimeric Rhinoviruses Displaying MPER Epitopes Elicit Anti-HIV Neutralizing Responses. PLOS ONE, 8(9), e72205. DOI: 10.1371/journal.pone.0072205. PMCID: PMC3765159.
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• Levy, Ronald M., Wei Dai, Nan-Jie Deng, and Dmitrii E. Makarov (2013). How long does it take to equilibrate the unfolded state of a protein?. Protein Science, 22(11), 1459-1465. DOI: 10.1002/pro.2335. PMCID: PMC3831662.
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• Wickstrom, Lauren, Peng He, Emilio Gallicchio, and Ronald M. Levy (2013). Large Scale Affinity Calculations of Cyclodextrin Host–Guest Complexes: Understanding the Role of Reorganization in the Molecular Recognition Process. J. Chem. Theory Comput., 9(7), 3136-3150. DOI: 10.1021/ct400003r. PMCID: PMC4137772.
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• Xia, Junchao, Nan-jie Deng, and Ronald M. Levy (2013). NMR Relaxation in Proteins with Fast Internal Motions and Slow Conformational Exchange: Model-Free Framework and Markov State Simulations. J. Phys. Chem. B, 117(22), 6625-6634. DOI: 10.1021/jp400797y. PMCID: PMC3727231.
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• Narayanan, Chitra, Daniel S. Weinstock, Kuen-Phon Wu, Jean Baum, and Ronald M. Levy (2012). Investigation of the Polymeric Properties of α-Synuclein and Comparison with NMR Experiments: A Replica Exchange Molecular Dynamics Study. J. Chem. Theory Comput., 8(10), 3929-3942. DOI: 10.1021/ct300241t. PMCID: PMC3496295.
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• Haq, Omar, Michael Andrec, Alexandre V. Morozov, and Ronald M. Levy (2012). Correlated Electrostatic Mutations Provide a Reservoir of Stability in HIV Protease. PLoS Computational Biology, 8(9), e1002675. DOI: 10.1371/journal.pcbi.1002675. PMCID: PMC3435258.
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• Gallicchio, Emilio and Ronald M. Levy (2012). Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM). Journal of Computer-Aided Molecular Design, 26(5), 505-516. DOI: 10.1007/s10822-012-9552-3. PMCID: PMC3383899.
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• Lapelosa, Mauro, Emilio Gallicchio, and Ronald M. Levy (2012). Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations. J. Chem. Theory Comput., 8(1), 47-60. DOI: 10.1021/ct200684b. PMCID: PMC3285237.
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• Wickstrom, Lauren, Emilio Gallicchio, and Ronald M. Levy (2012). The linear interaction energy method for the prediction of protein stability changes upon mutation. Proteins, 80(1), 111-125. DOI: 10.1002/prot.23168. PMCID: PMC3240711.
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• Tan, Zhiqiang, Emilio Gallicchio, Mauro Lapelosa, and Ronald M. Levy (2012). Theory of binless multi-state free energy estimation with applications to protein-ligand binding. J. Chem. Phys., 136(14), 144102. DOI: 10.1063/1.3701175. PMCID: PMC3339880.
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• Felts, Anthony K., Krystal LaBarge, Joseph D. Bauman, Dishaben V. Patel, Daniel M. Himmel, Eddy Arnold, Michael A. Parniak, and Ronald M. Levy (2011). Identification of Alternative Binding Sites for Inhibitors of HIV-1 Ribonuclease H Through Comparative Analysis of Virtual Enrichment Studies. Journal of Chemical Information and Modeling, 51(8), 1986-1998. DOI: 10.1021/ci200194w. PMCID: PMC3159817.
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• Deng, Nan-jie, Weihua Zheng, Emillio Gallicchio, and Ronald M. Levy (2011). Insights into the Dynamics of HIV-1 Protease: A Kinetic Network Model Constructed from Atomistic Simulations. J. Am. Chem. Soc., 133(24), 9387-9394. DOI: 10.1021/ja2008032. PMCID: PMC3116037.
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• Gallicchio, Emilio and Ronald M Levy (2011). Advances in all atom sampling methods for modeling protein–ligand binding affinities. Current Opinion in Structural Biology, 21(2), 161-166. DOI: 10.1016/j.sbi.2011.01.010. PMCID: PMC3070828.
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• Zheng, Weihua, Emilio Gallicchio, Nanjie Deng, Michael Andrec, and Ronald M. Levy (2011). Kinetic Network Study of the Diversity and Temperature Dependence of Trp-Cage Folding Pathways: Combining Transition Path Theory with Stochastic Simulations. J. Phys. Chem. B, 115(6), 1512-1523. DOI: 10.1021/jp1089596. PMCID: PMC3059588.
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• Gallicchio, Emilio and Ronald M. Levy (2011). Recent theoretical and computational advances for modeling protein–ligand binding affinities. Advances in Protein Chemistry and Structural Biology. Elsevier BV. DOI: 10.1016/b978-0-12-386485-7.00002-8. PMCID: PMC3445424.
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• Gallicchio, Emilio, Mauro Lapelosa, and Ronald M. Levy (2010). Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein-Ligand Binding Affinities. J. Chem. Theory Comput., 6(9), 2961-2977. DOI: 10.1021/ct1002913. PMCID: PMC2992355.
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• Okumura, Hisashi, Emilio Gallicchio, and Ronald M. Levy (2010). Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting. J. Comput. Chem., 31(7), 1357-1367. DOI: 10.1002/jcc.21419. PMCID: PMC2848294.
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• Lapelosa, Mauro, Gail Ferstandig Arnold, Emilio Gallicchio, Eddy Arnold, and Ronald M. Levy (2010). Antigenic Characteristics of Rhinovirus Chimeras Designed in silico for En5hanced Presentation of HIV-1 gp41 Epitopes. Journal of Molecular Biology, 397(3), 752-766. DOI: 10.1016/j.jmb.2010.01.064. PMCID: PMC2940250.
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• Frenkel, Yulia Volovik, Emilio Gallicchio, Kalyan Das, Ronald M. Levy, and Eddy Arnold (2009). Molecular Dynamics Study of Non-nucleoside Reverse Transcriptase Inhibitor 4-[[4-[[4-[( E )-2-Cyanoethenyl]-2,6-dimethylphenyl]amino]-2-pyrimidinyl]amino]benzonitrile (TMC278/Rilpivirine) Aggregates: Correlation between Amphiphilic Properties of the Drug and Oral Bioavailability. Journal of Medicinal Chemistry, 52(19), 5896-5905. DOI: 10.1021/jm900282z. PMCID: PMC2777543.
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• Paris, Kristina A., Omar Haq, Anthony K. Felts, Kalyan Das, Eddy Arnold, and Ronald M. Levy (2009). Conformational Landscape of the Human Immunodeficiency Virus Type 1 Reverse Transcriptase Non-Nucleoside Inhibitor Binding Pocket: Lessons for Inhibitor Design from a Cluster Analysis of Many Crystal Structures. Journal of Medicinal Chemistry, 52(20), 6413-6420. DOI: 10.1021/jm900854h. PMCID: PMC3182518.
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• Gallicchio, Emilio, Kristina Paris, and Ronald M. Levy (2009). The AGBNP2 Implicit Solvation Model. J. Chem. Theory Comput., 5(9), 2544-2564. DOI: 10.1021/ct900234u. PMCID: PMC2857935.
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• Wu, Kuen-Phon, Daniel S. Weinstock, Chitra Narayanan, Ronald M. Levy, and Jean Baum (2009). Structural Reorganization of α-Synuclein at Low pH Observed by NMR and REMD Simulations. Journal of Molecular Biology, 391(4), 784-796. DOI: 10.1016/j.jmb.2009.06.063. PMCID: PMC2766395.
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• Zheng, Weihua, Michael Andrec, Emilio Gallicchio, and Ronald M. Levy (2009). Recovering Kinetics from a Simplified Protein Folding Model Using Replica Exchange Simulations: A Kinetic Network and Effective Stochastic Dynamics. J. Phys. Chem. B, 113(34), 11702-11709. DOI: 10.1021/jp900445t. PMCID: PMC2975981.
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• Lapelosa, Mauro, Emilio Gallicchio, Gail Ferstandig Arnold, Eddy Arnold, and Ronald M. Levy (2009). In Silico Vaccine Design Based on Molecular Simulations of Rhinovirus Chimeras Presenting HIV-1 gp41 Epitopes. Journal of Molecular Biology, 385(2), 675-691. DOI: 10.1016/j.jmb.2008.10.089. PMCID: PMC2649764.
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• Haq, Omar, Ronald M Levy, Alexandre V Morozov, and Michael Andrec (2009). Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease. BMC Bioinformatics, 10(Suppl 8), S10. DOI: 10.1186/1471-2105-10-s8-s10. PMCID: PMC2745583.
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• Felts, A. K., M. Andrec, E. Gallicchio, and R. M. Levy (2009). Protein Folding and Binding: Effective Potentials, Replica Exchange Simulations, and Network Models. Biological and Medical Physics, Biomedical Engineering. Springer Science + Business Media. DOI: 10.1007/978-3-540-88787-4_5.
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• Felts, Anthony K., Emilio Gallicchio, Dmitriy Chekmarev, Kristina A. Paris, Richard A. Friesner, and Ronald M. Levy (2008). Prediction of Protein Loop Conformations Using the AGBNP Implicit Solvent Model and Torsion Angle Sampling. J. Chem. Theory Comput., 4(5), 855-868. DOI: 10.1021/ct800051k. PMCID: PMC2533438.
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• Weinstock, Daniel S., Chitra Narayanan, Jean Baum, and Ronald M. Levy (2008). Correlation between 13Cα chemical shifts and helix content of peptide ensembles. Protein Science, 17(5), 950-954. DOI: 10.1110/ps.073365408. PMCID: PMC2327285.
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• Knight, Jennifer L., Zhiyong Zhou, Emilio Gallicchio, Daniel M. Himmel, Richard A. Friesner, Eddy Arnold, and Ronald M. Levy (2008). Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling. Acta Cryst Sect D, 64(4), 383-396. DOI: 10.1107/s090744490800070x. PMCID: PMC2631124.
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• Zheng, Weihua, Michael Andrec, Emilio Gallicchi, and Ronald M. Levy (2008). Simple Continuous and Discrete Models for Simulating Replica Exchange Simulations of Protein Folding. The Journal of Physical Chemistry B, 112(19), 6083-6093. DOI: 10.1021/jp076377+. PMCID: PMC2978075.
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• Gallicchio, Emilio, Ronald M. Levy, and Manish Parashar (2008). Asynchronous replica exchange for molecular simulations. J. Comput. Chem., 29(5), 788-794. DOI: 10.1002/jcc.20839. PMCID: PMC2977925.
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• Zheng, W., M. Andrec, E. Gallicchio, and R. M. Levy (2007). Simulating replica exchange simulations of protein folding with a kinetic network model. Proceedings of the National Academy of Sciences, 104(39), 15340-15345. DOI: 10.1073/pnas.0704418104. PMCID: PMC2000486.
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• Zhou, Zhiyong, Anthony K. Felts, Richard A. Friesner, and Ronald M. Levy (2007). Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets. Journal of Chemical Information and Modeling, 47(4), 1599-1608. DOI: 10.1021/ci7000346. PMCID: PMC2547888.
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• Andrec, Michael, David A. Snyder, Zhiyong Zhou, Jasmine Young, Gaetano T. Montelione, and Ronald M. Levy (2007). A large data set comparison of protein structures determined by crystallography and NMR: Statistical test for structural differences and the effect of crystal packing. Proteins, 69(3), 449-465. DOI: 10.1002/prot.21507.
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• Weinstock, Daniel S., Chitra Narayanan, Anthony K. Felts, Michael Andrec, Ronald M. Levy, Kuen-Phon Wu, and Jean Baum (2007). Distinguishing among Structural Ensembles of the GB1 Peptide: REMD Simulations and NMR Experiments. J. Am. Chem. Soc., 129(16), 4858-4859. DOI: 10.1021/ja0677517.
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• Ravindranathan, Krishna Pratap, Emilio Gallicchio, Ann E. McDermott, and Ronald M. Levy (2007). Conformational Dynamics of Substrate in the Active Site of Cytochrome P450 BM-3/NPG Complex: Insights from NMR Order Parameters. J. Am. Chem. Soc., 129(3), 474-475. DOI: 10.1021/ja0672371.
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• Su, Yang, Emilio Gallicchio, Kalyan Das, Eddy Arnold, and Ronald M. Levy (2007). Linear Interaction Energy (LIE) Models for Ligand Binding in Implicit Solvent: Theory and Application to the Binding of NNRTIs to HIV-1 Reverse Transcriptase. J. Chem. Theory Comput., 3(1), 256-277. DOI: 10.1021/ct600258e.
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• Himmel, Daniel M., Stefan G. Sarafianos, Sanjeewa Dharmasena, Mohammed M. Hossain, Kessler McCoy-Simandle, Tatiana Ilina, Arthur D. Clark, Jennifer L. Knight, John G. Julias, Patrick K. Clark, Karsten Krogh-Jespersen, Ronald M. Levy, Stephen H. Hughes, Michael A. Parniak, and Eddy Arnold (2006). HIV-1 Reverse Transcriptase Structure with RNase H Inhibitor Dihydroxy Benzoyl Naphthyl Hydrazone Bound at a Novel Site. ACS Chem. Biol., 1(11), 702-712. DOI: 10.1021/cb600303y. PMCID: PMC2963427.
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• Ravindranathan, Krishna Pratap, Emilio Gallicchio, Richard A. Friesner, Ann E. McDermott, and Ronald M. Levy (2006). Conformational Equilibrium of Cytochrome P450 BM-3 Complexed with N-Palmitoylglycine: A Replica Exchange Molecular Dynamics Study. J. Am. Chem. Soc., 128(17), 5786-5791. DOI: 10.1021/ja058465i. PMCID: PMC2533527.
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• Zhang, Li, M. Parashar, E. Gallicchio, and R.M. Levy (2006). Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications. 2006 International Conference on Parallel Processing (ICPP '06). IEEE. DOI: 10.1109/icpp.2006.63.
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• Ravindranathan, Krishna Pratap, Emilio Gallicchio, and Ronald M. Levy (2005). Conformational Equilibria and Free Energy Profiles for the Allosteric Transition of the Ribose-binding Protein. Journal of Molecular Biology, 353(1), 196-210. DOI: 10.1016/j.jmb.2005.08.009.
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• Andrec, M., A. K. Felts, E. Gallicchio, and R. M. Levy (2005). Protein folding pathways from replica exchange simulations and a kinetic network model. Proceedings of the National Academy of Sciences, 102(19), 6801-6806. DOI: 10.1073/pnas.0408970102. PMCID: PMC1100763.
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• Gallicchio, Emilio, Michael Andrec, Anthony K. Felts, and Ronald M. Levy (2005). Temperature Weighted Histogram Analysis Method, Replica Exchange, and Transition Paths †. J. Phys. Chem. B, 109(14), 6722-6731. DOI: 10.1021/jp045294f.
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• Knight, Jennifer L., Vladimir Mekler, Jayanta Mukhopadhyay, Richard H. Ebright, and Ronald M. Levy (2005). Distance-Restrained Docking of Rifampicin and Rifamycin SV to RNA Polymerase Using Systematic FRET Measurements: Developing Benchmarks of Model Quality and Reliability. Biophysical Journal, 88(2), 925-938. DOI: 10.1529/biophysj.104.050187. PMCID: PMC1305165.
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• Andrec, Michael, Boris N. Kholodenko, Ronald M. Levy, and Eduardo Sontag (2005). Inference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracy. Journal of Theoretical Biology, 232(3), 427-441. DOI: 10.1016/j.jtbi.2004.08.022.
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• Banks, Jay L., Hege S. Beard, Yixiang Cao, Art E. Cho, Wolfgang Damm, Ramy Farid, Anthony K. Felts, Thomas A. Halgren, Daniel T. Mainz, Jon R. Maple, Robert Murphy, Dean M. Philipp, Matthew P. Repasky, Linda Y. Zhang, Bruce J. Berne, Richard A. Friesner, Emilio Gallicchio, and Ronald M. Levy (2005). Integrated Modeling Program, Applied Chemical Theory (IMPACT). J. Comput. Chem., 26(16), 1752-1780. DOI: 10.1002/jcc.20292. PMCID: PMC2742605.
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• Chekmarev, Dmitriy S., Tateki Ishida, and Ronald M. Levy (2004). Long-Time Conformational Transitions of Alanine Dipeptide in Aqueous Solution: Continuous and Discrete-State Kinetic Models. J. Phys. Chem. B, 108(50), 19487-19495. DOI: 10.1021/jp048540w.
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• Mukhopadhyay, Jayanta, Elena Sineva, Jennifer Knight, Ronald M. Levy, and Richard H. Ebright (2004). Antibacterial Peptide Microcin J25 Inhibits Transcription by Binding within and Obstructing the RNA Polymerase Secondary Channel. Molecular Cell, 14(6), 739-751. DOI: 10.1016/j.molcel.2004.06.010. PMCID: PMC2754415.
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• Felts, Anthony K., Yuichi Harano, Emilio Gallicchio, and Ronald M. Levy (2004). Free energy surfaces of β-hairpin and α-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model. Proteins, 56(2), 310-321. DOI: 10.1002/prot.20104.
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• Su, Yang and Emilio Gallicchio (2004). The non-polar solvent potential of mean force for the dimerization of alanine dipeptide: the role of solute–solvent van der Waals interactions. Biophysical Chemistry, 109(2), 251-260. DOI: 10.1016/j.bpc.2003.11.007.
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• Gallicchio, Emilio and Ronald M. Levy (2004). AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. J. Comput. Chem., 25(4), 479-499. DOI: 10.1002/jcc.10400.
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• Levy, Ronald M., Linda Y. Zhang, Emilio Gallicchio, and Anthony K. Felts (2003). On the Nonpolar Hydration Free Energy of Proteins: Surface Area and Continuum Solvent Models for the Solute-Solvent Interaction Energy. J. Am. Chem. Soc., 125(31), 9523-9530. DOI: 10.1021/ja029833a.
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• Andrec, Michael, Ronald M. Levy, and David S. Talaga (2003). Direct Determination of Kinetic Rates from Single-Molecule Photon Arrival Trajectories Using Hidden Markov Models. The Journal of Physical Chemistry A, 107(38), 7454-7464. DOI: 10.1021/jp035514+. PMCID: PMC2713777.
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• Du, P., M. Andrec, and R. M. Levy (2003). Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update. Protein Engineering Design and Selection, 16(6), 407-414. DOI: 10.1093/protein/gzg052.
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• Chernyavsky, B. (2003). The Rutgers Computational Grid: A Distributed Linux PC Cluster. Cluster Computing, 6(3), 267-278. DOI: 10.1023/a:1023544721955.
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• Felts, Anthony K., Emilio Gallicchio, Anders Wallqvist, and Ronald M. Levy (2002). Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the surface generalized born solvent model. Proteins: Structure, Function, and Genetics, 48(2), 404-422. DOI: 10.1002/prot.10171.
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• Kubo, Masahito, Ronald M. Levy, Peter J. Rossky, Nobuyuki Matubayasi, and Masaru Nakahara (2002). Chloride Ion Hydration and Diffusion in Supercritical Water Using a Polarizable Water Model. J. Phys. Chem. B, 106(15), 3979-3986. DOI: 10.1021/jp013743v.
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• Gallicchio, Emilio, Linda Yu Zhang, and Ronald M. Levy (2002). The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators. J. Comput. Chem., 23(5), 517-529. DOI: 10.1002/jcc.10045.
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• Mekler, Vladimir, Ekaterine Kortkhonjia, Jayanta Mukhopadhyay, Jennifer Knight, Andrei Revyakin, Achillefs N. Kapanidis, Wei Niu, Yon W. Ebright, Ronald Levy, and Richard H. Ebright (2002). Structural Organization of Bacterial RNA Polymerase Holoenzyme and the RNA Polymerase-Promoter Open Complex. Cell, 108(5), 599-614. DOI: 10.1016/s0092-8674(02)00667-0.
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• Wallqvist, Anders, Emilio Gallicchio, Anthony K. Felts, and Ronald M. Levy (2002). Detecting Native Protein Folds among Large Decoy Sets with the OPLS All-Atom Potential and the Surface Generalized Born Solvent Model. Advances in Chemical Physics. Wiley-Blackwell. DOI: 10.1002/0471224421.ch8.
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• Andrec, Michael and Ronald M. Levy (2002). Protein sequential resonance assignments by combinatorial enumeration using 13C-𝛼 chemical shifts and their (i, i-1) sequential connectivities. Journal of Biomolecular NMR, 23(4), 263-270. DOI: 10.1023/a:1020236105735.
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• Andrec, Michael, Yuichi Harano, Matthew P. Jacobson, Richard A. Friesner, and Ronald M. Levy (2002). Complete Protein Structure Determination using Backbone Residual Dipolar Couplings and Sidechain Rotamer Prediction. Journal of Structural and Functional Genomics, 2(2), 103-111. DOI: 10.1023/a:1020435630054.
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• Felts, Anthony K., Anders Wallqvist, Emilio Gallicchio, Donna Bassolino, Stanley R. Krystek, and Ronald M. Levy (2002). Fold Recognition using the OPLS All-Atom Potential and the Surface Generalized Born Solvent Model. Computational Methods for Macromolecules: Challenges and Applications. Springer Science + Business Media. DOI: 10.1007/978-3-642-56080-4_18.
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• Zhou, Ruhong, Richard A. Friesner, Avijit Ghosh, Robert C. Rizzo, William L. Jorgensen, and R. M. Levy (2001). New Linear Interaction Method for Binding Affinity Calculations Using a Continuum Solvent Model. J. Phys. Chem. B, 105(42), 10388-10397. DOI: 10.1021/jp011480z.
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• Wallqvist, Anders, Emilio Gallicchio, and Ronald M. Levy (2001). A Model for Studying Drying at Hydrophobic Interfaces: Structural and Thermodynamic Properties. J. Phys. Chem. B, 105(28), 6745-6753. DOI: 10.1021/jp010945i.
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• Zhang, Linda Yu, Emilio Gallicchio, Richard A. Friesner, and Ronald M. Levy (2001). Solvent models for protein-ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations. J. Comput. Chem., 22(6), 591-607. DOI: 10.1002/jcc.1031.
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• Andrec, Michael, Peicheng Du, and Ronald M. Levy (2001). Protein Structural Motif Recognition via NMR Residual Dipolar Couplings. J. Am. Chem. Soc., 123(6), 1222-1229. DOI: 10.1021/ja003979x.
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• Andrec, Michael, Peicheng Du, and Ronald M. Levy (2001). Protein Backbone Structure Determination Using only Residual Dipolar Couplings from One Ordering Medium. Journal of Biomolecular NMR, 21(4), 335-347. DOI: 10.1023/a:1013334513610.
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• Wallqvist, A., Y. Fukunishi, L. R. Murphy, A. Fadel, and R. M. Levy (2000). Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases. Bioinformatics, 16(11), 988-1002. DOI: 10.1093/bioinformatics/16.11.988.
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• Andrec, Michael, Keith G Inman, David J Weber, Ronald M Levy, and Gaetano T Montelione (2000). A Bayesian Statistical Method for the Detection and Quantification of Rotational Diffusion Anisotropy from NMR Relaxation Data. Journal of Magnetic Resonance, 146(1), 66-80. DOI: 10.1006/jmre.2000.2113.
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• Gallicchio, E., M. M. Kubo, and R. M. Levy (2000). Enthalpy-Entropy and Cavity Decomposition of Alkane Hydration Free Energies: Numerical Results and Implications for Theories of Hydrophobic Solvation. J. Phys. Chem. B, 104(26), 6271-6285. DOI: 10.1021/jp0006274.
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• Lockwood, Daren M., Peter J. Rossky, and Ronald M. Levy (2000). Functional Group Contributions to Partial Molar Compressibilities of Alcohols in Water. J. Phys. Chem. B, 104(17), 4210-4217. DOI: 10.1021/jp994197x.
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• Goodfellow, J (2000). Theory and simulation Editorial overview. Current Opinion in Structural Biology, 10(2), 137-138. DOI: 10.1016/s0959-440x(00)00081-6.
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• Murphy, L. R., A. Wallqvist, and R. M. Levy (2000). Simplified amino acid alphabets for protein fold recognition and implications for folding. Protein Engineering Design and Selection, 13(3), 149-152. DOI: 10.1093/protein/13.3.149.
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• Andrec, Michael, Gaetano T. Montelione, and Ronald M. Levy (2000). Lipari-Szabo Mapping: A Graphical Approach to Lipari-Szabo Analysis of NMR Relaxation Data using Reduced Spectral Density Mapping. Journal of Biomolecular NMR, 18(2), 83-100. DOI: 10.1023/a:1008302101116.
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• Andrec, Michael, Gaetano T. Montelione, and Ronald M. Levy (1999). Estimation of Dynamic Parameters from NMR Relaxation Data using the Lipari–Szabo Model-Free Approach and Bayesian Statistical Methods. Journal of Magnetic Resonance, 139(2), 408-421. DOI: 10.1006/jmre.1999.1839.
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• Zhang, Linda Yu, Emilio Gallicchio, and Ronald M. Levy (1999). Implicit solvent models for protein-ligand binding: Insights based on explicit solvent simulations. Simulation and theory of electrostatic interactions in solution. ASCE. DOI: 10.1063/1.1301542.
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• Murphy, Lynne Reed, Naiqi Li, Jean Baum, and Ronald M. Levy (1998). Tertiary Contacts in αa-Lactalbumin at pH 7 and pH 2: A Molecular Dynamics Study. Journal of Biomolecular Structure and Dynamics, 16(2), 355-365. DOI: 10.1080/07391102.1998.10508253.
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• Levy, Ronald M. and Emilio Gallicchio (1998). COMPUTER SIMULATIONS WITH EXPLICIT SOLVENT: Recent Progress in the Thermodynamic Decomposition of Free Energies and in Modeling Electrostatic Effects. Annu. Rev. Phys. Chem., 49(1), 531-567. DOI: 10.1146/annurev.physchem.49.1.531.
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• Gallicchio, Emilio, Masahito Mogami Kubo, and Ronald M. Levy (1998). Entropy-Enthalpy Compensation in Solvation and Ligand Binding Revisited. J. Am. Chem. Soc., 120(18), 4526-4527. DOI: 10.1021/ja974061h.
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• Goodfellow, JuliaM and RonaldM Levy (1998). Theory and simulation. Current Opinion in Structural Biology, 8(2), 209-210. DOI: 10.1016/s0959-440x(98)80040-7.
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• Murphy, Lynne Reed, Nobuyuki Matubayasi, Vilia A Payne, and Ronald M Levy (1998). Protein hydration and unfolding – insights from experimental partial specific volumes and unfolded protein models. Folding and Design, 3(2), 105-118. DOI: 10.1016/s1359-0278(98)00016-9.
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• Matubayasi, Nobuyuki, Emilio Gallicchio, and Ronald M. Levy (1998). On the local and nonlocal components of solvation thermodynamics and their relation to solvation shell models. J. Chem. Phys., 109(12), 4864. DOI: 10.1063/1.477097.
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• Jin, Danqing, Michael Andrec, Gaetano T. Montelione, and Ronald M. Levy (1998). Propagation of Experimental Uncertainties Using the Lipari-Szabo Model-Free Analysis of Protein Dynamics. Journal of Biomolecular NMR, 12(4), 471-492. DOI: 10.1023/a:1008313319334.
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• Kubo, Masahito Mogami, Emilio Gallicchio, and Ronald M. Levy (1997). Thermodynamic Decomposition of Hydration Free Energies by Computer Simulation: Application to Amines, Oxides, and Sulfides. J. Phys. Chem. B, 101(49), 10527-10534. DOI: 10.1021/jp972598b.
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• Jin, Danqing, Francisco Figueirido, Gaetano T. Montelione, and Ronald M. Levy (1997). Impact of the Precision in NMR Relaxation Measurements on the Interpretation of Protein Dynamics. Journal of the American Chemical Society, 119(29), 6923-6924. DOI: 10.1021/ja970947+.
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• Figueirido, Francisco, Gabriela S. Del Buono, and Ronald M. Levy (1997). On Finite-Size Corrections to the Free Energy of Ionic Hydration. J. Phys. Chem. B, 101(29), 5622-5623. DOI: 10.1021/jp970882x.
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• Payne, Vilia Ann, Nobuyuki Matubayasi, Lynne Reed Murphy, and Ronald M. Levy (1997). Monte Carlo Study of the Effect of Pressure on Hydrophobic Association. J. Phys. Chem. B, 101(11), 2054-2060. DOI: 10.1021/jp962977p.
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• Figueirido, Francisco, Ronald M. Levy, Ruhong Zhou, and B. J. Berne (1997). Large scale simulation of macromolecules in solution: Combining the periodic fast multipole method with multiple time step integrators. J. Chem. Phys., 106(23), 9835. DOI: 10.1063/1.474115.
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• Buono, Gabriela S. Del, Francisco E. Figueirido, and Ronald M. Levy (1996). Dielectric response of solvent surrounding an ion pair: Ewald potential versus spherical truncation. Chemical Physics Letters, 263(3-4), 521-529. DOI: 10.1016/s0009-2614(96)01234-1.
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• Figueirido, Francisco, Gabriela S. Del Buono, and Ronald M. Levy (1996). Prediction of p K a Shifts without Truncation of Electrostatic Interactions: An Explicit Solvent Calculation for Succinic Acid. J. Phys. Chem., 100(16), 6389-6392. DOI: 10.1021/jp9600524.
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• Matubayasi, Nobuyuki and Ronald M. Levy (1996). Thermodynamics of the Hydration Shell. 2. Excess Volume and Compressibility of a Hydrophobic Solute. J. Phys. Chem., 100(7), 2681-2688. DOI: 10.1021/jp951618b.
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• Fadel, AddiR., DanQ. Jin, GaetanoT. Montelione, and RonaldM. Levy (1995). Crankshaft motions of the polypeptide backbone in molecular dynamics simulations of human type-? transforming growth factor. J Biomol NMR, 6(2). DOI: 10.1007/bf00211787.
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• Bernardo, Dan N., Yanbo Ding, Karsten Krogh-Jespersen, and Ronald M. Levy (1995). Evaluating polarizable potentials on distributed memory parallel computers: Program development and applications. J. Comput. Chem., 16(9), 1141-1152. DOI: 10.1002/jcc.540160908.
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• Ding, Yanbo, Dan N. Bernardo, Karsten Krogh-Jespersen, and Ronald M. Levy (1995). Solvation Free Energies of Small Amides and Amines from Molecular Dynamics/Free Energy Perturbation Simulations Using Pairwise Additive and Many-Body Polarizable Potentials. J. Phys. Chem., 99(29), 11575-11583. DOI: 10.1021/j100029a040.
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• Suri, A.K. and R.M. Levy (1995). A Relaxation-Matrix Analysis of Distance-Constraint Ranges for NOEs in Proteins at Long Mixing Times. Journal of Magnetic Resonance, Series B, 106(1), 24-31. DOI: 10.1006/jmrb.1995.1004.
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• Figueirido, Francisco, Gabriela S. Del Buono, and Ronald M. Levy (1995). On finite-size effects in computer simulations using the Ewald potential. J. Chem. Phys., 103(14), 6133. DOI: 10.1063/1.470721.
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• Matubayasi, Nobuyuki, Lynne H. Reed, and Ronald M. Levy (1994). Thermodynamics of the Hydration Shell. 1. Excess Energy of a Hydrophobic Solute. J. Phys. Chem., 98(41), 10640-10649. DOI: 10.1021/j100092a040.
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• Buono, Gabriela S. Del, Francisco E. Figueirido, and Ronald M. Levy (1994). Intrinsic pKas of ionizable residues in proteins: An explicit solvent calculation for lysozyme. Proteins: Structure, Function, and Genetics, 20(1), 85-97. DOI: 10.1002/prot.340200109.
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• Figueirido, Francisco, Gabriela S. Del Buono, and Ronald M. Levy (1994). Molecular mechanics and electrostatic effects. Biophysical Chemistry, 51(2-3), 235-241. DOI: 10.1016/0301-4622(94)00044-1.
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• Chen, Yuan, AsifK. Suri, Dorothea Kominos, Gautam Sanyal, AdelM. Naylor, StevenM. Pitzenberger, VictorM. Garsky, RonaldM. Levy, and Jean Baum (1994). Three-dimensional structure of echistatin and dynamics of the active site. J Biomol NMR, 4(3). DOI: 10.1007/bf00179342.
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• Bernardo, Dan N., Yanbo Ding, Karsten Krogh-Jespersen, and Ronald M. Levy (1994). An Anisotropic Polarizable Water Model: Incorporation of All-Atom Polarizabilities into Molecular Mechanics Force Fields. J. Phys. Chem., 98(15), 4180-4187. DOI: 10.1021/j100066a043.
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• Suri, A.K. and R.M. Levy (1993). Estimation of Interatomic Distances in Proteins from NOE Spectra at Longer Mixing Times Using an Empirical Two-Spin Equation. Journal of Magnetic Resonance, Series B, 101(3), 320-324. DOI: 10.1006/jmrb.1993.1050.
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• Smith, Maureen J., Karsten Krogh-Jespersen, and Ronald M. Levy (1993). Solvent effects on the torsional dynamics of a twisted intramolecular charge transfer (TICT) molecule: bianthryl in acetonitrile. Chemical Physics, 171(1-2), 97-106. DOI: 10.1016/0301-0104(93)85134-t.
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• Alper, Howard and Ronald M. Levy (1993). Dielectric and thermodynamic response of a generalized reaction field model for liquid state simulations. J. Chem. Phys., 99(12), 9847. DOI: 10.1063/1.465468.
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• Smith-Brown, Maureen J., Dorothea Kominos, and Ronald M. Levy (1993). Global folding of proteins using a limited number of distance constraints. Protein Eng Des Sel, 6(6), 605-614. DOI: 10.1093/protein/6.6.605.
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• Westbrook, John D., Ronald M. Levy, and Karsten Krogh-Jespersen (1992). Molecular electrostatic potentials and partial atomic charges from correlated wave functions: Applications to the electronic ground and excited states of 3-methylindole. J. Comput. Chem., 13(8), 979-989. DOI: 10.1002/jcc.540130808.
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• Kitchen, Douglas B., Lynne H. Reed, and Ronald M. Levy (1992). Molecular dynamics simulation of solvated protein at high pressure. Biochemistry, 31(41), 10083-10093. DOI: 10.1021/bi00156a031.
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• Kominos, Dorothea, Asif K Suri, Douglas B Kitchen, Donna Bassolino, and Ronald M Levy (1992). Simulating the effect of the two-spin approximation on the generation of protein structures from NOE data. Journal of Magnetic Resonance (1969), 97(2), 398-410. DOI: 10.1016/0022-2364(92)90325-2.
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• Westbrook, John D., Ronald M. Levy, and Karsten Krogh-Jespersen (1992). . Time-Resolved Laser Spectroscopy in Biochemistry III. SPIE. DOI: 10.1117/12.58196.
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• Figueirido, Francisco E. and Ronald M. Levy (1992). Vibrational relaxation and Bloch–Redfield theory. J. Chem. Phys., 97(1), 703. DOI: 10.1063/1.463566.
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• Fan, Pei, Dorothea Kominos, Douglas B. Kitchen, Ronald M. Levy, and Jean Baum (1991). Stabilization of α-helical secondary structure during high-temperature molecular-dynamics simulations of α-lactalbumin. Chemical Physics, 158(2-3), 295-301. DOI: 10.1016/0301-0104(91)87073-5.
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• Levy, Ronald M., John D. Westbrook, Douglas B. Kitchen, and Karsten Krogh-Jespersen (1991). Solvent effects on the adiabatic free energy difference between the ground and excited states of methylindole in water. J. Phys. Chem., 95(18), 6756-6758. DOI: 10.1021/j100171a005.
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• Belhadj, Mahfoud, Howard E. Alper, and Ronald M. Levy (1991). Molecular dynamics simulations of water with Ewald summation for the long range electrostatic interactions. Chemical Physics Letters, 179(1-2), 13-20. DOI: 10.1016/0009-2614(91)90284-g.
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• Belhadj, Mahfoud, Douglas B. Kitchen, Karsten Krogh-Jespersen, and Ronald M. Levy (1991). A molecular dynamics study of pressure effects on solvation and optical spectra: the ground and excited states of formaldehyde in water. J. Phys. Chem., 95(3), 1082-1089. DOI: 10.1021/j100156a013.
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• Levy, Ronald M., Mahfoud Belhadj, and Douglas B. Kitchen (1991). Gaussian fluctuation formula for electrostatic free-energy changes in solution. J. Chem. Phys., 95(5), 3627. DOI: 10.1063/1.460813.
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• Kominos, Dorothea, Donna A. Bassolino, Ronald M. Levy, and Arthur Pardi (1990). Analysis of side-chain conformational distributions in neutrophil peptide-5 nmr structures. Biopolymers, 29(14), 1807-1822. DOI: 10.1002/bip.360291412.
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• Alper, Howard E. and Ronald M. Levy (1990). Field strength dependence of dielectric saturation in liquid water. J. Phys. Chem., 94(22), 8401-8403. DOI: 10.1021/j100385a008.
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• Kitchen, Douglas B., Fumio Hirata, John D. Westbrook, Ronald Levy, David Kofke, and Martin Yarmush (1990). Conserving energy during molecular dynamics simulations of water, proteins, and proteins in water. J. Comput. Chem., 11(10), 1169-1180. DOI: 10.1002/jcc.540111009.
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• Metzler, William J., Chuan Wang, Douglas B. Kitchen, Ronald M. Levy, and Arthur Pardi (1990). Determining local conformational variations in DNA. Journal of Molecular Biology, 214(3), 711-736. DOI: 10.1016/0022-2836(90)90288-w.
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• Levy, Ronald M., Douglas B. Kitchen, John T. Blair, and Karsten. Krogh-Jespersen (1990). Molecular dynamics simulation of time-resolved fluorescence and nonequilibrium solvation of formaldehyde in water. J. Phys. Chem., 94(11), 4470-4476. DOI: 10.1021/j100374a023.
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• Blair, John T., Ronald M. Levy, and Karsten Krogh-Jespersen (1990). Molecular mechanics parameters for electronically excited states: The (n, π∗) singlet state of formaldehyde. Chemical Physics Letters, 166(4), 429-436. DOI: 10.1016/0009-2614(90)85056-i.
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• Perahia, D., R. M. Levy, and M. Karplus (1990). Motions of an ?-helical polypeptide: Comparison of molecular and harmonic dynamics. Biopolymers, 29(4-5), 645-677. DOI: 10.1002/bip.360290402.
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• Levy, Ronald M., Donna A. Bassolino, Douglas B. Kitchen, and Arthur Pardi (1989). Solution structures of proteins from NMR data and modeling: alternative folds for neutrophil peptide 5. Biochemistry, 28(24), 9361-9372. DOI: 10.1021/bi00450a017.
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• Blair, John T., Karsten Krogh-Jespersen, and Ronald M. Levy (1989). Solvent effects on optical absorption spectra: the 1A1 .fwdarw. 1A2 transition of formaldehyde in water. J. Am. Chem. Soc., 111(18), 6948-6956. DOI: 10.1021/ja00200a009.
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• Blair, John T., John D. Westbrook, Ronald M. Levy, and Karsten Krogh-Jespersen (1989). Simple models for solvation effects on electronic transition energies: Formaldehyde and water. Chemical Physics Letters, 154(6), 531-535. DOI: 10.1016/0009-2614(89)87146-5.
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• Hirata, Fumio and Ronald M. Levy (1989). Salt-induced conformational changes in DNA: analysis using the polymer RISM theory. J. Phys. Chem., 93(1), 479-484. DOI: 10.1021/j100338a092.
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• Alper, Howard, Donna Bassolino, John T. Blair, Douglas B. Kitchen, Dorothea Kominos, and Ronald M. Levy (1989). Supercomputer Simulations of Solvation in Chemistry and Biochemistry: From Ions to Proteins. In: "John Von Neumann Supercomputer Center Annual Report to the National Science Foundation". .
  
• Alper, Howard E. and Ronald M. Levy (1989). Computer simulations of the dielectric properties of water: Studies of the simple point charge and transferrable intermolecular potential models. J. Chem. Phys., 91(2), 1242. DOI: 10.1063/1.457198.
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• Levy, R. M. (1988). Biomolecular Processes: Dynamics of Proteins and Nucleic Acids.. Science, 241(4862), 234-235. DOI: 10.1126/science.241.4862.234.
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• Bassolino, D. A., F. Hirata, D. B. Kitchen, D. Kominos, A. Pardi, and R. M. Levy (1988). Determination of Protein Structures in Solution Using Nmr Data and Impact. International Journal of High Performance Computing Applications, 2(2), 41-61. DOI: 10.1177/109434208800200204.
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• Hirata, Fumio, Paul Redfern, and Ronald M. Levy (1988). Viewing the born model for ion hydration through a microscope. Int. J. Quantum Chem., 34(S15), 179-190. DOI: 10.1002/qua.560340716.
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• Zhang, Peisen, Ronald M. Levy, and Richard A. Friesner (1988). Variable quadratic propagator for quantum Monte Carlo simulations. Chemical Physics Letters, 144(3), 236-242. DOI: 10.1016/0009-2614(88)87147-1.
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• Levy, Ronald M. (1988). New Computational Methods for Protein Structure Determination in Solution. In: "John Von Neumann Supercomputer Center Annual Report to the National Science Foundation". .
  
• Levy, Ronald M., Fumio Hirata, Kwang Kim, and Peisen Zhang (1987). Using Computer Simulations To Probe the Structure and Dynamics of Biopolymers. Supercomputer Research in Chemistry and Chemical Engineering. American Chemical Society (ACS). DOI: 10.1021/bk-1987-0353.ch006.
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• Hirata, Fumio. and Ronald M. Levy (1987). Ionic association in methanol and related solvents: an extended RISM analysis. J. Phys. Chem., 91(18), 4788-4795. DOI: 10.1021/j100302a028.
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• Hirata, Fumio and Ronald M. Levy (1987). A new RISM integral equation for solvated polymers. Chemical Physics Letters, 136(3-4), 267-273. DOI: 10.1016/0009-2614(87)80249-x.
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• Friesner, Richard A. and Ronald M. Levy (1987). Theoretical Methods for Studying Collective Modes in Proteins. Biological applications of Raman Spectroscopy, Vol. 1---Raman Spectra and The Conformations of Biological Macromolecules. John Wiley and Sons.
  
• Levy, Ronald M. (1986). Computer Simulations of Macromolecular Dynamics: Models for Vibrational Spectroscopy and X-Ray Refinement. Annals of the New York Academy of Sciences, 482(1 Computer Simu), 24-43. DOI: 10.1111/j.1749-6632.1986.tb20934.x.
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• Weiner, Paul K, Steven L Gallion, Eric Westhof, and Ronald M Levy (1986). Visualization of energetics and conformations from molecular computer simulations. Journal of Molecular Graphics, 4(4), 203-207. DOI: 10.1016/0263-7855(86)80041-8.
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• Westhof, Eric, Bernard Chevrier, Steven L. Gallion, Paul K. Weiner, and Ronald M. Levy (1986). Temperature-dependent molecular dynamics and restrained X-ray refinement simulations of a Z-DNA hexamer. Journal of Molecular Biology, 191(4), 699-712. DOI: 10.1016/0022-2836(86)90454-7.
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• Kuriyan, John, Gregory A. Petsko, Ronald M. Levy, and Martin Karplus (1986). Effect of anisotropy and anharmonicity on protein crystallographic refinement. Journal of Molecular Biology, 190(2), 227-254. DOI: 10.1016/0022-2836(86)90295-0.
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• Gallion, Steven L., Ronald M. Levy, Paul K. Weiner, and Fumio Hirata (1986). Implementation of a macromolecular mechanics program on a cyber 205 supercomputer. Computers {\&} Chemistry, 10(3), 165-173. DOI: 10.1016/0097-8485(86)80008-0.
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• Levy, Ronald M. and J. Keepers (1986). Computer Simulations of Protein Dynamics: Theory and Experiment. Comments on Molecular and Cellular Biophysics. Gordon and Breach Science Publishers.
  
• Levy, Ronald M. (1986). Using Macromolecular Dynamics Simulations to Interpret Experiments. Israel Journal of Chemistry, 27(2), 173-179. DOI: 10.1002/ijch.198600026.
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• Rojas, Olivia L., Ronald M. Levy, and Attila Szabo (1986). Corrections to the quasiharmonic approximation for evaluating molecular entropies. J. Chem. Phys., 85(2), 1037. DOI: 10.1063/1.451296.
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• Levy, R.M., R.P. Sheridan, J.W. Keepers, G.S. Dubey, S. Swaminathan, and M. Karplus (1985). Molecular dynamics of myoglobin at 298 degrees K. Results from a 300-ps computer simulation. Biophysical Journal, 48(3), 509-518. DOI: 10.1016/s0006-3495(85)83806-6. PMCID: PMC1329364.
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• Levy, Ronald M. (1985). Quasiharmonic Methods for Classical and Quantum Simulations. In: "Molecular Dynamics and Protein Structure: Workshop Proceedings". J. Hermans ed. U. North Carolina,.
  
• Levy, Ronald M. (1985). NMR Relaxation and the Dynamics of Proteins. In: "Molecular Dynamics and Protein Structure: Workshop Proceedings". J. Hermans ed. U. North Carolina,.
  
• Levy, Ronald M., Olivia De la Luz Rojas, and Richard A. Friesner (1984). Quasi-harmonic method for calculating vibrational spectra from classical simulations on multi-dimensional anharmonic potential surfaces. J. Phys. Chem., 88(19), 4233-4238. DOI: 10.1021/j150663a009.
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• Levy, Ronald M., Martin Karplus, Joseph Kushick, and David Perahia (1984). Evaluation of the configurational entropy for proteins: application to molecular dynamics simulations of an α-helix. Macromolecules, 17(7), 1370-1374. DOI: 10.1021/ma00137a013.
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• Levy, R. M., A. R. Srinivasan, W. K. Olson, and J. A. McCammon (1984). Quasi-harmonic method for studying very low frequency modes in proteins. Biopolymers, 23(6), 1099-1112. DOI: 10.1002/bip.360230610.
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• Olejniczak, E. T., C. M. Dobson, M. Karplus, and R. M. Levy (1984). Motional averaging of proton nuclear Overhauser effects in proteins. Predictions from a molecular dynamics simulation of lysozyme. J. Am. Chem. Soc., 106(7), 1923-1930. DOI: 10.1021/ja00319a004.
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• Friesner, Richard A. and Ronald M. Levy (1984). An optimized harmonic reference system for the evaluation of discretized path integrals. J. Chem. Phys., 80(9), 4488. DOI: 10.1063/1.447232.
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• Sheridan, R. P., R. M. Levy, and S. W. Englander (1983). Normal mode paths for hydrogen exchange in the peptide ferrichrome. Proceedings of the National Academy of Sciences, 80(18), 5569-5572. DOI: 10.1073/pnas.80.18.5569.
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• Levy, Ronald M. and Martin Karplus (1983). Trajectory Studies of NMR Relaxation in Flexible Molecules. Molecular-Based Study of Fluids. American Chemical Society (ACS). DOI: 10.1021/ba-1983-0204.ch018.
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• Levy, R.M. and R.P. Sheridan (1983). Combined effect of restricted rotational diffusion plus jumps on nuclear magnetic resonance and fluorescence probes of aromatic ring motions in proteins. Biophysical Journal, 41(2), 217-221. DOI: 10.1016/s0006-3495(83)84422-1. PMCID: PMC1329169.
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• Lipari, Giovanni, Attila Szabo, and Ronald M. Levy (1982). Protein dynamics and NMR relaxation: comparison of simulations with experiment. Nature, 300(5888), 197-198. DOI: 10.1038/300197a0.
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• Sheridan, R. P., R. M. Levy, and F. R. Salemme (1982). 𝛼-Helix dipole model and electrostatic stabilization of 4-𝛼-helical proteins.. Proceedings of the National Academy of Sciences, 79(15), 4545-4549. DOI: 10.1073/pnas.79.15.4545.
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• Levy, R.M., C.M. Dobson, and M. Karplus (1982). Dipolar NMR relaxation of nonprotonated aromatic carbons in proteins. Structural and dynamical effects. Biophysical Journal, 39(1), 107-113. DOI: 10.1016/s0006-3495(82)84496-2. PMCID: PMC1328916.
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• Levy, Ronald M. and Attila Szabo (1982). Initial fluorescence depolarization of tyrosines in proteins. J. Am. Chem. Soc., 104(7), 2073-2075. DOI: 10.1021/ja00371a070.
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• Levy, R. M., D. Perahia, and M. Karplus (1982). Molecular dynamics of an 𝛼-helical polypeptide: Temperature dependence and deviation from harmonic behavior. Proceedings of the National Academy of Sciences, 79(4), 1346-1350. DOI: 10.1073/pnas.79.4.1346.
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• Levy, Ronald M., Martin Karplus, and Peter G. Wolynes (1981). NMR relaxation parameters in molecules with internal motion: exact Langevin trajectory results compared with simplified relaxation models. J. Am. Chem. Soc., 103(20), 5998-6011. DOI: 10.1021/ja00410a002.
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• Pear, Michael R., Scott H. Northrup, J. Andrew McCammon, Martin Karplus, and Ronald M. Levy (1981). Correlated helix-coil transitions in polypeptides. Biopolymers, 20(3), 629-632. DOI: 10.1002/bip.1981.360200314.
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• Levy, Ronald M., Martin Karplus, and J. Andrew McCammon (1981). Increase of carbon-13 NMR relaxation times in proteins due to picosecond motional averaging. J. Am. Chem. Soc., 103(4), 994-996. DOI: 10.1021/ja00394a072.
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• McCammon, J. A., S. H. Northrup, M. Karplus, and R. M. Levy (1980). Helix-coil transitions in a simple polypeptide model. Biopolymers, 19(11), 2033-2045. DOI: 10.1002/bip.1980.360191108.
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• Levy, Ronald M., Martin Karplus, and J.Andrew McCammon (1980). Molecular dynamics studies of nmr relaxation in proteins. Biophysical Journal, 32(1), 628-630. DOI: 10.1016/s0006-3495(80)84998-8.
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• Levy, Ronald M., Martin Karplus, and J. Andrew McCammon (1980). Molecular Dynamics Studies of NMR Relaxation in proteins. In: "Proteins and Nucleoproteins Structure, Dynamics and Assembly". V.A. Parsegian, Ed., Rockefeller University Press, New York, NY.
  
• Levy, Ronald M. and Martin Karplus (1979). Vibrational approach to the dynamics of an 𝛼-helix. Biopolymers, 18(10), 2465-2495. DOI: 10.1002/bip.1979.360181008.
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• Levy, Ronald M., Martin Karplus, and J. Andrew McCammon (1979). Diffusive langevin dynamics of model alkanes. Chemical Physics Letters, 65(1), 4-11. DOI: 10.1016/0009-2614(79)80114-1.
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• Levy, Ronald M. (1979). Diffusive Dynamics of Alkane Chains. Report of 1978 Workshop "Stochastic Methods in Macromolecular Dynamics". Centre European de Calcul Atomique et Moleculaire, University de Paris IX, France.
  
• Levy, Ronald M. (1979). Langevin Simulation of Liquid State Alkane Dynamics. Report of 1979 NCAA Workshop "Stochastic Molecular Dynamics". National Resources for Computation in Chemistry, Lawrence Berkeley Laboratory, U. of California, Berkeley, CA.
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• Levy, Ronald M. and Martin J. Kushmerick (1977). Induction of contractile activity by rigor complexes in myofibrils. Biochemical and Biophysical Research Communications, 76(2), 512-519. DOI: 10.1016/0006-291x(77)90754-9.
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• Levy, Ronald M., Yoshiki Umazume, and Martin J. Kushmerick (1976). Ca2+ dependence of tension and ADP production in segments of chemically skinned muscle fibers. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 430(2), 352-365. DOI: 10.1016/0005-2728(76)90091-8.
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