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Ronald M. Levy

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Ronald M. Levy

  • College of Science and Technology

    • Chemistry

      • Laura H. Carnell Professor

Courses Taught

Number

Name

Level

CHEM 5412

Structural Bioinformatics II

Graduate

Selected Publications

Recent

  • McGee, F., Hauri, S., Novinger, Q., Vucetic, S., Levy, R., Carnevale, V., & Haldane, A. (2021). The generative capacity of probabilistic protein sequence models. Nature Communications, 12(1). doi: 10.1038/s41467-021-26529-9.

  • Arasteh, S., Zhang, B., & Levy, R. (2021). Protein Loop Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates. Journal of Physical Chemistry Letters, 12(18), 4368-4377. doi: 10.1021/acs.jpclett.1c00778.

  • Haldane, A. & Levy, R. (2021). Mi3-GPU: MCMC-based inverse Ising inference on GPUs for protein covariation analysis. Computer Physics Communications, 260. doi: 10.1016/j.cpc.2020.107312.

  • Sun, Q., Ramaswamy, V., Levy, R., & Deng, N. (2021). 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: 10.1002/pro.4004.

  • Sun, Q., Levy, R., Kirby, K., Wang, Z., Sarafianos, S., & Deng, N. (2021). Molecular dynamics free energy simulations reveal the mechanism for the antiviral resistance of the m66i hiv-1 capsid mutation. Viruses, 13(5). doi: 10.3390/v13050920.

  • Do, H., Haldane, A., Levy, R., & Miao, Y. (2021). Unique features of different classes of G-protein-coupled receptors revealed from sequence coevolutionary and structural analysis. Proteins: Structure, Function and Bioinformatics. doi: 10.1002/prot.26256.

  • Levy, R., Matubayasi, N., & Zhang, B. (2020). Solvation Thermodynamics from the Perspective of Endpoints DFT. Journal of Physical Chemistry B, 124(52), 11771-11782. doi: 10.1021/acs.jpcb.0c08988.

  • Tse, C., Wickstrom, L., Kvaratskhelia, M., Gallicchio, E., Levy, R., & Deng, N. (2020). Exploring the Free-Energy Landscape and Thermodynamics of Protein-Protein Association. Biophysical Journal, 119(6), 1226-1238. doi: 10.1016/j.bpj.2020.08.005.

  • Zhang, B., Matubayasi, N., & Levy, R. (2020). Cavity Particle in Aqueous Solution with a Hydrophobic Solute: Structure, Energetics, and Functionals. Journal of Physical Chemistry B, 124(25), 5220-5237. doi: 10.1021/acs.jpcb.0c02721.

  • Narayan, B., Fathizadeh, A., Templeton, C., He, P., Arasteh, S., Elber, R., Buchete, N., & Levy, R. (2020). The transition between active and inactive conformations of Abl kinase studied by rock climbing and Milestoning. Biochimica Et Biophysica Acta - General Subjects, 1864(4). doi: 10.1016/j.bbagen.2019.129508.

  • Levy, R. (2020). Insights into the energy landscapes of chromosome organization proteins from coevolutionary sequence variation and structural modeling. Proceedings of the National Academy of Sciences of the United States of America, 117(5), 2241-2242. doi: 10.1073/pnas.1921727117.

  • Cui, D., Zhang, B., Tan, Z., & Levy, R. (2020). Ligand Binding Thermodynamic Cycles: Hysteresis, the Locally Weighted Histogram Analysis Method, and the Overlapping States Matrix. Journal of Chemical Theory and Computation, 16(1), 67-79. doi: 10.1021/acs.jctc.9b00740.

  • Sakae, Y., Zhang, B., Levy, R., & Deng, N. (2020). 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.

  • Zhang, B., Arasteh, S., & Levy, R. (2019). The UWHAM and SWHAM Software Package. Scientific Reports, 9(1). doi: 10.1038/s41598-019-39420-x.

  • Biswas, A., Haldane, A., Arnold, E., & Levy, R. (2019). Epistasis and entrenchment of drug resistance in HIV-1 subtype B. ELife, 8. doi: 10.7554/eLife.50524.

  • Ishii, Y., Yamamoto, N., Matubayasi, N., Zhang, B., Cui, D., & Levy, R. (2019). Spatially-Decomposed Free Energy of Solvation Based on the Endpoint Density-Functional Method. Journal of Chemical Theory and Computation, 15(5), 2896-2912. doi: 10.1021/acs.jctc.8b01309.

  • Koneru, P., Francis, A., Deng, N., Rebensburg, S., Hoyte, A., Lindenberger, J., Adu-Ampratwum, D., Larue, R., Wempe, M., Engelman, A., Lyumkis, D., Fuchs, J., Levy, R., Melikyan, G., & Kvaratskhelia, M. (2019). Hiv-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors. ELife, 8. doi: 10.7554/eLife.46344.

  • Xia, J., Flynn, W., Gallicchio, E., Uplinger, K., Armstrong, J., Forli, S., Olson, A., & Levy, R. (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.

  • Haldane, A. & Levy, R. (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.

  • Arasteh, S., He, P., Haldane, A., & Levy, R.M. (2019). Protein Kinase Free Energy Landscapes: The Role of the Activation Loop. BIOPHYSICAL JOURNAL, 116(3), 436A-436A. 10.1016/j.bpj.2018.11.2348

  • Haldane, A., He, P., Flynn, W.F., & Levy, R.M. (2019). Coevolutionary Landscapes of Kinase Family Proteins. BIOPHYSICAL JOURNAL, 116(3), 168A-168A. 10.1016/j.bpj.2018.11.936

  • He, P., Zhang, B., Arasteh, S., Wang, L., Abel, R., & Levy, R.M. Protein Conformational Free Energy Changes Via an Alchemical Pathway. PROTEIN SCIENCE, 27, 244-245. Retrieved from http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000450682700455&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=abcd71df5a6dac31fd219478b0a9c638.

  • He, P., Zhang, B., Arasteh, S., Wang, L., Abel, R., & Levy, R. (2018). Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates. Journal of Physical Chemistry Letters, 9(15), 4428-4435. doi: 10.1021/acs.jpclett.8b01851.

  • Xia, J., Flynn, W., & Levy, R. (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.

  • Zhang, B., Cui, D., Matubayasi, N., & Levy, R. (2018). The Excess Chemical Potential of Water at the Interface with a Protein from End Point Simulations. Journal of Physical Chemistry B, 122(17), 4700-4707. doi: 10.1021/acs.jpcb.8b02666.

  • Cui, D., Zhang, B., Matubayasi, N., & Levy, R. (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.

  • Haldane, A., Flynn, W., He, P., & Levy, R. (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.

  • Deng, N., Cui, D., Zhang, B., Xia, J., Cruz, J., & Levy, R. (2018). Comparing alchemical and physical pathway methods for computing the absolute binding free energy of charged ligands. Physical Chemistry Chemical Physics, 20(25), 17081-17092. doi: 10.1039/c8cp01524d.

  • Zhang, B., Deng, N., Tan, Z., & Levy, R. (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.

  • Harris, R., Deng, N., Levy, R., Ishizuka, R., & Matubayasi, N. (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(15), 1198-1208. doi: 10.1002/jcc.24668.

  • Flynn, W., Haldane, A., Torbett, B., & Levy, R. (2017). Inference of epistatic effects leading to entrenchment and drug resistance in HIV-1 protease. Molecular Biology and Evolution, 34(6), 1291-1306. doi: 10.1093/molbev/msx095.

  • Levy, R., Cui, D., Zhang, B., & Matubayasi, N. (2017). Relationship between Solvation Thermodynamics from IST and DFT Perspectives. Journal of Physical Chemistry B, 121(15), 3825-3841. doi: 10.1021/acs.jpcb.6b12889.

  • Post, C. & Levy, R. (2017). Editorial overview: Theory & computation. Current Opinion in Structural Biology, 43, iv-vi. doi: 10.1016/j.sbi.2017.04.008.

  • Levy, R., Haldane, A., & Flynn, W. (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.

  • Pal, R., Haider, K., Kaur, D., Flynn, W., Xia, J., Levy, R., Taran, T., Wickstrom, L., Kurtzman, T., & Gallicchio, E. (2017). Erratum to: 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, (2017), 31, 1, (29-44), 10.1007/s10822-016-9956-6). Journal of Computer-Aided Molecular Design, 31(1), 45. doi: 10.1007/s10822-016-9987-z.

  • Pal, R., Haider, K., Kaur, D., Flynn, W., Xia, J., Levy, R., Taran, T., Wickstrom, L., Kurtzman, T., & Gallicchio, E. (2017). 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, 31(1), 29-44. doi: 10.1007/s10822-016-9956-6.