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De novo discovery of peptide-based affinity ligands for the fab fragment of human immunoglobulin G

. JOURNAL OF CHROMATOGRAPHY A, 1669. https://doi.org/10.1016/j.chroma.2022.462941 Sarma, S., Herrera, S. M., Xiao, X., Hudalla, G. A., & Hall, C. K. (2022). Computational Design and Experimental Validation of ACE2-Derived Peptides as SARS-CoV-2 Receptor Binding Domain Inhibitors. JOURNAL OF PHYSICAL CHEMISTRY B, 126(41), 8129–8139. https://doi.org/10.1021/acs.jpcb.2c039188129J Xiao, X., Robang, A. S., Sarma, S., Le, J. V., Helmicki, M. E., Lambert, M. J., … Hall, C. K. (2022). Sequence patterns and signatures: Computational and experimental discovery of amyloid-forming peptides. PNAS NEXUS, 1(5). https://doi.org/10.1093/pnasnexus/pgac263 Xiao, X., Wang, Y., Seroski, D. T., Wong, K. M., Liu, R., Paravastu, A. K., … Hall, C. K. (2021). De novo design of peptides that coassemble into beta sheet-based nanofibrils. SCIENCE ADVANCES, 7(36). https://doi.org/10.1126/sciadv.abf7668 Wong, K. M., Robang, A. S., Lint, A. H., Wang, Y., Dong, X., Xiao, X., … Paravastu, A. K. (2021, December 14). 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Insights into the solvation and dynamic behaviors of a lithium salt in organic- and ionic liquid-based electrolytes. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 21(35), 19216–19225. https://doi.org/10.1039/c9cp01848d Xiao, X., Kuang, Z., Slocik, J. M., Tadepalli, S., Brothers, M., Kim, S., … Naik, R. R. (2018). Advancing Peptide-Based Biorecognition Elements for Biosensors Using in-Silico Evolution. ACS SENSORS, 3(5), 1024–1031. https://doi.org/10.1021/acssensors.8b00159 Zhou, X., Su, Z., Chen, H., Xiao, X., Qin, Y., Yang, L., … Sun, W. (2018). Capture of pure toxic gases through porous materials from molecular simulations. MOLECULAR PHYSICS, Vol. 116, pp. 2095–2107. https://doi.org/10.1080/00268976.2018.1440019 Kang, H., Xiao, X., Huang, C., Yuan, Y., Tang, D., Dai, X., & Zeng, X. (2018). Potent aromatase inhibitors and molecular mechanism of inhibitory action. EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 143, 426–437. https://doi.org/10.1016/j.ejmech.2017.11.057 Xiao, X., Wang, Y., Leonard, J. N., & Hall, C. K. (2017). Extended Concerted Rotation Technique Enhances the Sampling Efficiency of the Computational Peptide-Design Algorithm. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 13(11), 5709–5720. https://doi.org/10.1021/acs.jctc.7b00714 Xiao, X., Hung, M. E., Leonard, J. N., & Hall, C. K. (2016). Adding energy minimization strategy to peptide-design algorithm enables better search for RNA-binding peptides: Redesigned N peptide binds boxB RNA. JOURNAL OF COMPUTATIONAL CHEMISTRY, 37(27), 2423–2435. https://doi.org/10.1002/jcc.24466 Xu, X., Xiao, X., Xu, S., & Liu, H. (2016). Computational insights into the destabilization of alpha-helical conformations formed by leucine zipper peptides in response to temperature. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18(36), 25465–25473. https://doi.org/10.1039/c6cp05145f Xiao, X., Agris, P. F., & Hall, C. K. (2016). Introducing folding stability into the score function for computational design of RNA-binding peptides boosts the probability of success. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 84(5), 700–711. https://doi.org/10.1002/prot.25021 Xiao, X., Zhao, B., Yang, L., Liang, X., & Ren, Y. (2016). Probe the Binding Mode of Aristololactam-beta-D-glucoside to Phenylalanine Transfer RNA in Silico. CHEMISTRYSELECT, 1(17), 5430–5439. https://doi.org/10.1002/slct.201600603 Xiao, X., Zhao, B., Agris, P. F., & Hall, C. K. (2016). Simulation study of the ability of a computationally-designed peptide to recognize target tRNA(Lys3) and other decoy tRNAs. PROTEIN SCIENCE, 25(12), 2243–2255. https://doi.org/10.1002/pro.3056 Xiao, X., Agris, P. F., & Hall, C. K. (2015). Designing Peptide Sequences in Flexible Chain Conformations to Bind RNA: A Search Algorithm Combining Monte Carlo, Self-Consistent Mean Field and Concerted Rotation Techniques. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11(2), 740–752. https://doi.org/10.1021/ct5008247 Xiao, X., Zhao, B., & Ren, Y. (2015). Effect of curvature on properties of diblock copolymers confined between two coaxial cylinders: 1. Layer thickness of a curved monolayer. CHEMICAL PHYSICS LETTERS, 633, 58–64. https://doi.org/10.1016/j.cplett.2015.05.016 Xiao, X., Zhao, B., Yang, L., & Ren, Y. (2015). Effect of curvature on properties of diblock copolymers confined between two coaxial cylinders: 2. Domain adjustment in a curved bilayer. CHEMICAL PHYSICS LETTERS, 639, 326–334. https://doi.org/10.1016/j.cplett.2015.10.032 Xiao, X., Agris, P. F., & Hall, C. K. (2015). Molecular recognition mechanism of peptide chain bound to the tRNA(Lys3) anticodon loop in silico. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33(1), 14–27. https://doi.org/10.1080/07391102.2013.869660 Curtis, E. M., Xiao, X., Sofou, S., & Hall, C. K. (2015). Phase Separation Behavior of Mixed Lipid Systems at Neutral and Low pH: Coarse-Grained Simulations with DMD/LIME. LANGMUIR, 31(3), 1086–1094. https://doi.org/10.1021/la504082x Spears, J. L., Xiao, X., Hall, C. K., & Agris, P. F. (2014). Amino Acid Signature Enables Proteins to Recognize Modified tRNA. Biochemistry, 53(7), 1125–1133. https://doi.org/10.1021/bi401174h Xiao, X., Hall, C. K., & Agris, P. F. (2014). The design of a peptide sequence to inhibit HIV replication: a search algorithm combining Monte Carlo and self-consistent mean field techniques. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32(10), 1523–1536. https://doi.org/10.1080/07391102.2013.825757