Proteins

Displaying 1 - 17 of 17CSV
Fisher, R. S., Liao, J., Ahn, S. Y., Modi, N., Kidane, A. K., & Obermeyer, A. C. (2025). Engineering Protein–Polyelectrolyte Interactions for Cellular Applications. Annual Review of Chemical and Biomolecular Engineering, 16(1), 119–145. https://doi.org/10.1146/annurev-chembioeng-100722-105929
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Liao, J., Sergeeva, A. P., Harder, E. D., Wang, L., Sampson, J. M., Honig, B., & Friesner, R. A. (2024). A Method for Treating Significant Conformational Changes in Alchemical Free Energy Simulations of Protein–Ligand Binding. Journal of Chemical Theory and Computation, 20(19), 8609–8623. https://doi.org/10.1021/acs.jctc.4c00954
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Sampson, J. M., Cannon, D. A., Duan, J., Epstein, J. C. K., Sergeeva, A. P., Katsamba, P. S., Mannepalli, S. M., Bahna, F. A., Adihou, H., Guéret, S. M., Gopalakrishnan, R., Geschwindner, S., Rees, D. G., Sigurdardottir, A., Wilkinson, T., Dodd, R. B., De Maria, L., Mobarec, J. C., Shapiro, L., … Wang, L. (2024). Robust Prediction of Relative Binding Energies for Protein–Protein Complex Mutations Using Free Energy Perturbation Calculations. Journal of Molecular Biology, 436(16), 168640. https://doi.org/10.1016/j.jmb.2024.168640
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Rodriguez, D. C. P., Weber, K. C., Sundberg, B., & Glasgow, A. (2024). MAGPIE: An interactive tool for visualizing and analyzing protein–ligand interactions. Protein Science, 33(8). Portico. https://doi.org/10.1002/pro.5027
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Feng, H., Lu, X.-J., Maji, S., Liu, L., Ustianenko, D., Rudnick, N. D., & Zhang, C. (2024). Structure-based prediction and characterization of photo-crosslinking in native protein–RNA complexes. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-46429-y
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Li, S., Bhattacharya, S., Chou, C.-Y., Chu, M., Chou, S.-C., Tonelli, M., Goger, M., Yang, H., Palmer, A. G., & Cavagnero, S. (2024). LC-Photo-CIDNP hyperpolarization of biomolecules bearing a quasi-isolated spin pair: Magnetic-Field dependence via a rapid-shuttling device. Journal of Magnetic Resonance, 359, 107616. https://doi.org/10.1016/j.jmr.2023.107616
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Roy, R., Geng, A., Shi, H., Merriman, D. K., Dethoff, E. A., Salmon, L., & Al-Hashimi, H. M. (2023). Kinetic Resolution of the Atomic 3D Structures Formed by Ground and Excited Conformational States in an RNA Dynamic Ensemble. Journal of the American Chemical Society, 145(42), 22964–22978. https://doi.org/10.1021/jacs.3c04614
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Watson, J. L., Juergens, D., Bennett, N. R., Trippe, B. L., Yim, J., Eisenach, H. E., Ahern, W., Borst, A. J., Ragotte, R. J., Milles, L. F., Wicky, B. I. M., Hanikel, N., Pellock, S. J., Courbet, A., Sheffler, W., Wang, J., Venkatesh, P., Sappington, I., Torres, S. V., … Baker, D. (2023). De novo design of protein structure and function with RFdiffusion. Nature, 620(7976), 1089–1100. https://doi.org/10.1038/s41586-023-06415-8
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Kesner, J. S., Chen, Z., Shi, P., Aparicio, A. O., Murphy, M. R., Guo, Y., Trehan, A., Lipponen, J. E., Recinos, Y., Myeku, N., & Wu, X. (2023). Noncoding translation mitigation. Nature, 617(7960), 395–402. https://doi.org/10.1038/s41586-023-05946-4
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Trudeau, S. J., Hwang, H., Mathur, D., Begum, K., Petrey, D., Murray, D., & Honig, B. (2023). PrePCI: A structure‐ and chemical similarity‐informed database of predicted protein compound interactions. Protein Science, 32(4). Portico. https://doi.org/10.1002/pro.4594
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Du, D. X., Simjanoska, M., & Fitzpatrick, A. W. P. (2023). Four-dimensional microED of conformational dynamics in protein microcrystals on the femto-to-microsecond timescales. Journal of Structural Biology, 215(1), 107941. https://doi.org/10.1016/j.jsb.2023.107941
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Maráková, K., Renner, B. J., Thomas, S. L., Opetová, M., Tomašovský, R., Rai, A. J., & Schug, K. A. (2023). Solid phase extraction as sample pretreatment method for top-down quantitative analysis of low molecular weight proteins from biological samples using liquid chromatography – triple quadrupole mass spectrometry. Analytica Chimica Acta, 1243, 340801. https://doi.org/10.1016/j.aca.2023.340801
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Fan, X., Pan, H., Tian, A., Chung, W. K., & Shen, Y. (2022). SHINE: protein language model-based pathogenicity prediction for short inframe insertion and deletion variants. Briefings in Bioinformatics, 24(1). https://doi.org/10.1093/bib/bbac584
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de Prisco, N., Botta, S., Lee, W., Rezazadeh, S., Chemiakine, A., & Gennarino, V. A. (2022). Determining the effects of loss of function mutations in human cell lines. STAR Protocols, 3(2), 101232. https://doi.org/10.1016/j.xpro.2022.101232
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