Publications

At Kentucky

2024

(1) Wang D., Pourmirzaei M., Abbas U. L., Zeng S., Manshour N., Esmaili F., Poudel B., Jiang Y., Shao Q., Chen J., Xu D., S-PLM: Structure-Aware Protein Language Model via Contrastive Learning Between Sequence and Structure. Adv. Sci. 2024, 2404212. https://doi.org/10.1002/advs.202404212

(2) Imam, I. A., Shatha A. A., Liu X. L., Ellingson S., Brainson C. F., Moseley H., Zinner R., Zhang S., and Shao Q. L858R/L718Q and L858R/L792H Mutations of EGFR Inducing Resistance Against Osimertinib by Forming Additional Hydrogen Bonds. Proteins: Structure, Function, and Bioinformatics, 2024, doi.org/10.1002/prot.26761

(3) Li, C.; Allison, D. B.; He, D.; Mao, F.; Wang, X.; Rychahou, P.; Imam, I. A.; Kong, Y.; Zhang, Q.; Zhang, Y.; Liu, J.; Wang, R.; Rao, X.; Wu, S.; Evers, B. M.; Shao, Q.; Wang, C.; Li, Z.; Liu, X. Phosphorylation of AHR by PLK1 promotes metastasis of LUAD via DIO2-TH signaling. PLoS Genetics 2023, 19 (11), e1011017.

(4) Abbas, U. L., Zhang YX, Tapia J., Selim Md, Chen, J., Shi, J., Shao, Q. Machine Learning-Assisted Design of Deep Eutectic Solvents Based on Uncovered Hydrogen Bond Patterns, Engineering, 2024, 39,74-83.

(5) Pan, X., Liu Y., Ma Z., Qin Y., Lu X, Feng X, Shao Q., and Zhu Y.. Molecular insight into the mechanism of lignin dissolution in acid choline chloride–Based deep eutectic solvents. Journal of Molecular Liquids (2024): 125123.

(6) Zhang, Y., Hunter. J., Ullah A, Shao Q, and Shi J., Lignin derived hydrophobic deep eutectic solvents for the extraction of nanoplastics from water. Journal of Hazardous Materials 467 (2024): 133695.

2023
(1) Hunter, J., Qiao Q., Zhang Y., Shao Q., Crofcheck C., and Shi J., Green solvent mediated extraction
of micro-and nano-plastic particles from water. Scientific Reports 13, no. 1 (2023): 10585.

(2) Abbas, U. L., Chen, J., Shao, Q. (2023). Assessing Fairness of AlphaFold2 Prediction of Protein 3D Structures. ACM-BCB 2023 - 14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics.

(3) Nguyen, M. T.; Abbas, U. L.; Qi, Q.; Shao, Q. Distinct Effect of Zwitterionic Molecules on Ionic Solvation in (Ethylene Oxide)10: a Molecular Dynamics Simulation Study. Physical Chemistry Chemical Physics 2023, 10.1039/D2CP02301F

(4) Nguyen, M.T; Lee Y.-L.; Alfonso D.;Shao Q.; Y. H.; Description of Reaction and Vibrational Energetics of CO2-NH3 Interaction Using Quantum Computing Algorithms, AVS Quantum Science, 2023, Accepted (feature article).

(5) Ullah, A.; Zhang, Y.; Liu, C.; Qiao, Q.; Shao, Q.; Shi, J., Process intensification strategies for green solvent mediated biomass pretreatment. Bioresource Technology 2023, 369, 128394.

2022
(1) Zhang, Y.; Qiao, Q.; Abbas, U. L.; Liu, J.; Zheng, Y.; Jones, C.; Shao, Q.; Shi, J., Lignin derived hydrophobic deep eutectic solvents as sustainable extractants. Journal of Cleaner Production 2022, 135808.

(2) Zhang Z, Cheng L, Li J, Qiao Q, Karki A, Allison DB, Shaker N, Li K, Utturkar SM, Atallah Lanman NM, Rao X, Rychahou P, He D, Konieczny SF, Wang C, Shao Q, Evers BM, Liu X. Targeting Plk1 Sensitizes Pancreatic Cancer to Immune Checkpoint Therapy. Cancer Res. 2022 Oct 4;82(19):3532-
3548. doi: 10.1158/0008-5472.CAN-22-0018. PMID: 35950917; PMCID: PMC9532376.

(3) McMullen, P.; Fang, L.; Qiao, Q.; Shao, Q.; Jiang, S., Impacts of a Zwitterionic Peptide on its Fusion Protein. Bioconjugate Chemistry 2022, 33 (8), 1485-1493.

(4) Qiao, Q.; Cai, L.; Shao, Q., Molecular simulations of zwitterlation-induced conformation and dynamics variation of glucagon-like peptide-1 and insulin. Journal of Materials Chemistry B 2022, 10 (14), 2490-2496.

(5) McMullen, P.; Qiao, Q.; Luozhong, S.; Cai, L.; Fang, L.; Shao, Q.; Jiang, S., Motif-based zwitterionic peptides impact their structure and immunogenicity. Chemical Science 2022.

(6) Xu, L.; Xu, N.; Wang, L.; Qian, H.; Li, Y.; Fang, M.; Xiang, Z.; Lin, W.; Zhang, F.; Shao, Q., Spontaneously Restoring Specific Bioaffinity of RGD in Linear RGD-containing Peptides by Conjugation with Zwitterionic Dendrimers. Acta biomaterialia 2022, 148, 61-72.

(7) Zhang, Z.; Cheng, L.; Li, J.; Qiao, Q.; Karki, A.; Allison, D. B.; Shaker, N.; Li, K.; Utturkar, S. M.; Atallah Lanman, N. M., Targeting Plk1 sensitizes pancreatic cancer to immune checkpoint therapy. Cancer Research 2022. doi.org/10.1158/0008-5472.CAN-22-0018

2021:

(6) Abbas, UL, Qiao, Q, Nguyen, MT, Shi, J, Shao, Q.* Structure and hydrogen bonds of hydrophobic deep eutectic solvent-aqueous liquid–liquid interfaces. AIChE J. 2021; 67( 12):e17427. doi:10.1002/aic.17427

(7) Abbas, UL, Qiao, Q, Nguyen, MT, Shi, J, Shao, Q.* Molecular dynamics simulations of heterogeneous hydrogen bond environment in hydrophobic deep eutectic solvents. AIChE J. 2022; 68( 1):e17382. https://doi.org/10.1002/aic.17382

(8) Qiao Q, Shi J, Shao Q.* The multiscale solvation effect on the reactivity of β-O-4 of lignin dimers in deep eutectic solvents. Physical Chemistry Chemical Physics. 2021;23(45):25699-705. doi: 10.1039/D1CP04342K.

(9) Qiao Q, Shi J, Shao Q.* Effects of water on the solvation and structure of lipase in deep eutectic solvents containing a protein destabilizer and stabilizer. Physical Chemistry Chemical Physics. 2021;23(40):23372-9. doi: 10.1039/D1CP03282H.

(10) Wong KM, Shao Q, Wang Y, Seroski DT, Liu R, Lint AH, Hudalla GA, Hall CK, Paravastu AK. CATCH Peptides Coassemble into Structurally Heterogeneous β-Sheet Nanofibers with Little Preference to β-Strand Alignment. J. Phys. Chem. B. 2021. Doi.org/10.1021/acs.jpcb.0c11645

(11) Chen, A.B., Shao, Q. and Hall, C.K.*, Molecular simulation study of 3, 4-dihydroxyphenylalanine in the context of underwater adhesive design. J. Chem. Phys., 2021, 154, 144702.

(12) Ding J, Xu N, Nguyen MT, Qiao Q, Shi Y, He Y*, Shao Q*. Machine learning for molecular thermodynamics. Chin. J. Chem. Eng., 2021. https://doi.org/10.1016/j.cjche.2020.10.044.

(13) Chen X, Li C, Bernards MT, Shi Y, Shao Q, He Y.* Sequence-based peptide identification, generation, and property prediction with deep learning: a review. Molecular Systems Design & Engineering. 2021;6(6):406-28. doi: 10.1039/D0ME00161A.

2020:

(14) Cheng, L., Ji, Y.* and Shao, Q., 2020. Facile modification of hydrochar derived from cotton straw with excellent sorption performance for antibiotics: Coupling DFT simulations with experiments. Sci. Total Environ., 2020, 760, 144124.

(15) Seroski, D.T., Dong, X., Wong, K.M., Liu, R., Shao, Q., Paravastu, A.K., Hall, C.K. and Hudalla, G.A.*, Charge guides pathway selection in β-sheet fibrillizing peptide co-assembly. Commun. Chem, 2020, 3, 1-11.

(16) Xu N., Shi Y, He Y*, and Shao Q*. A Deep-Learning Potential for Crystalline and Amorphous Li-Si Alloys, J. Phys. Chem. C, 2020, 124, 12678-12688

(17) Shao Q* Effect of Conjugated (EK)10 Peptide on Structural and Dynamic Properties of Ubiquitin Protein: a Molecular Dynamics Simulation Study, J. Mater. Chem. B, 2020, 8, 6934-6943

(18) Nguyen, M. T, Shao Q* Effects of zwitterionic molecules on ionic association in ethylene oxide-based electrolytes, Fluid Phase Equil. 2020, 515, 112572

(19) Nguyen, M. T, Shao Q*. Effect of Zwitterionic Molecules on Ionic Transport under Electric Fields: A Molecular Simulation Study, J. Chem. Eng. Data, 2020, 65, 2, 385–395

(20) Shao Q(co first-author), Wong KM (co first-author), Seroski D. T. (co first-author), Wang Y. M., Liu R. J., Paravastu A. K., Hudalla G. A., and Hall C. K.*., Anatomy of a Selectively Co-assembled β-sheet Peptide Nanofiber, Proc. Natl. Acad. Sci. U.S.A. 2020, 117, 4710-4717

2019:

(21) Shao Q.*; A Computational Avenue towards Understanding and Design of Zwitterionic Anti-biofouling Materials Mol. Simul. 2019, 1-12.

Before Kentucky

(1) Han X, Leng C., Shao Q, Jiang S. Y., Chen Z, Absolute Orientations of Water Molecules at Zwitterionic Polymer Interfaces and Interfacial Dynamics after Salt Exposure Langmuir, 2019, 355, 1327-1334

(2) Shao Q.; Hall C. K., Selectivity of Glycine for Facets on Gold Nanoparticles J. Phys. Chem. B, 2017, 122, 13, 3491-3499

(3) Shao Q.; Hall C. K., Allosteric Effects of Gold Nanoparticle on Human Serum Albumin, Nanoscale 2017, 9(1):380-390

(4) Shao Q.; Hall C. K., Binding Preferences of Amino Acids for Gold Nanoparticles: a Molecular Simulation Study. Langmuir 2016, 32(31):7888-7896

(5) Shao Q.; Hall C. K., Protein Adsorption on Nanoparticles: Model Development Using Computer Simulation J. Phys. Conden. Matter. 2016 28(41):414019

(6) Shao Q.; Hall C. K., A Discontinuous-Potential Model for Protein-Protein Interactions, Molecular Modeling and Simulation: Applications and Perspectives 2016:1-20

(7) Wang Y. M., Shao Q., and Hall C. K., N-terminal Prion Protein Peptides (PrP120-144) Form Parallel In-register β-sheets via Multiple Nucleation-dependent Pathways, J. Biol. Chem. 291(42):22093-22105.

(8) Zhao, Y.; Bai, T., Shao, Q., Jiang, S. Y., Shen Q. A., Thermoresponsive self-assembled NiPAm-zwitterion copolymers, Polym. Chem., 2015, 6, 1066-1077.

(9) Shao, Q.; Jiang, S. Y., Molecular Understanding and Design of Zwitterionic Materials. Adv. Mater. 2015,27(1):15-26.

(10) Shao, Q.; Jiang, S. Y., Influence of Charged Groups on Properties of Zwitterionic Moieties: A Molecular Simulation Study. J. Phys. Chem. B, 2014, 118 (27): 7630–7637.

(11) Shao, Q.; Mi L., Bai T., Han X., Liu S., Li Y. T.; and Jiang S. Y., Differences in Cationic and Anionic Charge Densities Dictate Zwitterionic Associations and Stimuli Responses. J. Phys. Chem. B, 2014, 118 (24): 6956–6962.

(12) Shao, Q.; White, A. D.; Jiang, S. Y., Difference of Carboxybetaine and Oligo(ethylene glycol) Moieties in Altering Hydrophobic Interactions: A Molecular Simulation Study. J. Phys. Chem. B, 2014, 118(1): 189-194.

(13) Bai, T.; Liu, S.; Sun, F.; Sinclair, A.; Zhang, L.; Shao, Q.; Jiang, S. Y., Zwitterionic Fusion in Hydrogels and Spontaneous and Time-independent Self-healing under Physiological Conditions. Biomaterials 2014, 35(13), 3926-3933

(14) Mi L.; White A. D.; Shao Q.; Setlow P.; Li Y. Q.; Jiang S. Y.; Chemical Insights into Dodecylamine Spore Lethal Germination. Chem. Sci. 2014, 5, 3320-3324.

(15) Leng C.; Han, X. F.; Shao, Q.; Zhu, Y. H.; Li, Y. T.; Jiang, S. Y.; Chen, Z. In situ Probing the Surface Hydration of Zwitterionic Polymer Brushes: Structural and Environmental Effects. J. Phys. Chem. C, 2014, 118 (29): 15840–15845.

(16) Sundaram, H. S.; Ella-Menye, J. R.; Brault N. D.; Shao Q.; Jiang S. Y., Reversibly Switchable Polymer with Cationic/Zwitterionic/Anionic Behavior through Synergistic Protonation and Deprotonation. Chem. Sci., 2014, 5(1): 200-205.

(17) Shao, Q.; Jiang, S. Y., Effects of Carbon Spacer Length on Zwitterionic Carboxybetaines. J. Phys. Chem. B, 2013,117 (5): 1357–1366.

(18) White, A. D.; Keefe, A. J.; Ella-Menye, J.-R.; Nowinski, A. K.; Shao, Q.; Pfaendtner, J.; Jiang, S., Free Energy of Solvated Salt Bridges: A Simulation and Experimental Study. J. Phys. Chem. B, 2013, 117 (24): 7254-7259.

(19) White, A. D.; Keefe, A. J.; Nowinski, A. K.; Shao, Q.; Caldwell, K.; Jiang, S., Standardizing and Simplifying Analysis of Peptide Library Data. J. Chem. Inf. Model. 2013, 53 (2): 493-499.

(20) Shao, Q.; He, Y.; White, A. D.; Jiang, S. Y., Different Effects of Zwitterion and Ethylene Glycol on Proteins. J. Chem. Phys., 2012, 136 (22): 225101.

(21) Mi, L.; Giarmarco, M. M.; Shao, Q.; Jiang, S. Y., Divalent Cation-mediated Polysaccharide Interactions with Zwitterionic Surfaces. Biomaterials 2012, 33 (7): 2001-2006.

(22) Shao, Q.; He, Y.; Jiang, S. Y., Molecular Dynamics Simulation Study of Ion Interactions with Zwitterions. J. Phys. Chem. B, 2011, 115 (25): 8358-8363.

(23) He, Y.; Shao, Q.; Tsao, H. K.; Chen, S. F.; Goddard, W. A.; Jiang, S. Y., Understanding Three Hydration-Dependent Transitions of Zwitterionic Carboxybetaine Hydrogel by Molecular Dynamics Simulations. J. Phys. Chem. B, 2011, 115 (40): 11575-11580.

(24) He, Y.; Shao, Q.; Chen, S. F.; Jiang, S. Y., Water Mobility: A Bridge between the Hofmeister Series of Ions and the Friction of Zwitterionic Surfaces in Aqueous Environments. J. Phys. Chem. C, 2011, 115 (31): 15525-15531.

(25) He, Y.; Shao, Q.; Chen, S. F.; Jiang, S. Y., Chaotrope vs. Kosmotrope: Which One Has Lower Friction? J. Chem. Phys. 2011, 135 (15): 154702 .

(26) Shao, Q.; He, Y.; White, A. D.; Jiang, S. Y., Difference in Hydration between Carboxybetaine and Sulfobetaine. J. Phys. Chem. B, 2010, 114 (49): 16625-16631.

(27) Zhu, Y. D.; Guo, X. J.; Shao, Q.; Wei, M. J.; Wu, X. M.; Lu, L. H.; Lu, X. H., Molecular Simulation Study of the Effect of Inner Wall Modified Groups on Ionic Hydration Confined in Carbon Nanotube. Fluid Phase Equilib. 2010, 297 (2): 215-220.

(28) Guo, X. J.; Shao, Q.; Lu, L. H.; Zhu, Y. D.; Wei, M. J.; Lu, X. H., Molecular Dynamics Simulation Study of Ionic Hydration in Negatively Charged Single-Walled Carbon Nanotubes. J. Nanosci. Nanotechnol. 2010, 10 (11): 7620-7624.

(29) Shao, Q.; Zhou, J.; Lu, L. H.; Lu, X. H.; Zhu, Y. D.; Jiang, S. Y., Anomalous Hydration Shell Order of Na+ and K+ inside Carbon Nanotubes. Nano Letters 2009, 9 (3): 989-994.

(30) Zhu, Y. D.; Wei, M. J.; Shao, Q.; Lu, L. H.; Lu, X. H.; Shen, W. F., Molecular Dynamics Study of Pore Inner Wall Modification Effect in Structure of Water Molecules Confined in Single-Walled Carbon Nanotubes. J. Phys. Chem. C 2009, 113 (3): 882-889.

(31) Liu, C.; Ji, Y.; Shao, Q.; Feng, X.; Lu, X. In Molecular Therodynamics of Complex Systems; Lu, X., Hu, Y., Eds. 2009; Vol. 131, p 193.

(32) Shao, Q.; Lu, L. H.; Lu, X. H.; Wei, M. J.; Zhu, Y. D.; Shen, W. F., Molecular Simulation of Solute Hydration Structure in Nanoscale Confinement. Acta Physico-Chimica Sinica 2009, 25 (3): 583-589.

(33) Shao, Q.; Huang, L. L.; Zhou, J.; Lu, L. H.; Zhang, L. Z.; Lu, X. H.; Jiang, S. Y.; Gubbins, K. E.; Shen, W. F., Molecular Simulation Study of Temperature Effect on Ionic Hydration in Carbon Nanotubes. Phys. Chem. Chem. Phys. 2008, 10 (14): 1896-1906.

(34) Shao, Q.; Huang, L. L.; Zhou, J.; Lu, L. H.; Zhang, L. Z.; Lu, X. H.; Jiang, S. Y.; Gubbins, K. E.; Zhu, Y. D.; Shen, W. F., Molecular Dynamics Study on Diameter Effect in Structure of Ethanol Molecules Confined in Single-walled Carbon Nanotubes. J. Phys. Chem. B, 2007, 111 (43): 15677-15685.

(35) Shao, Q.; Huang, L. L.; Lu, X. H.; Lu, L. H.; Zhu, Y. D.; Shen, W. F., Molecular Simulation Study of the Structure and Diffusion of Ethanol Molecules Confined in Carbon Nanotubes. Acta Chimica Sinica 2007, 65 (20): 2217-2223.

(36) Lu, L. H.; Shao, Q.; Huang, L. L.; Lu, X. H., Simulation of Adsorption and Separation of Ethanol-Water Mixture with Zeolite and Carbon Nanotube. Fluid Phase Equilib. 2007, 261 (1-2): 191-198;

(37) Lu, L. H.; Lu, X. H.; Chen, Y. P.; Huang, L. L.; Shao, Q.; Wang, Q., Monte Carlo Simulation of Adsorption of Binary and Quaternary Alkane Isomers Mixtures in Zeolites: Effect of Pore Size and Structure. Fluid Phase Equilib. 2007, 259 (2): 135-145.

(38) Huang, L. L.; Zhang, L. Z.; Shao, Q.; Lu, L. H.; Lu, X. H.; Jiang, S. Y.; Shen, W. F., Simulations of Binary Mixture Adsorption of Carbon Dioxide and Methane in Carbon Nanotubes: Temperature, Pressure, and Pore Size Effects. J. Phys. Chem. C, 2007, 111 (32): 11912-11920.

(39) Chen, Y. P.; Lu, L. H.; Shao, Q.; Huang, L. L.; Lu, X. H., Adsorption and Diffusion of Alkanes in Mordenite. Acta Physico-Chimica Sinica 2007, 23 (6): 905-910.

(40) Huang, L. L.; Zhang, L. Z.; Shao, Q.; Wang, J.; Lu, L. H.; Lu, X. H.; Jiang, S. Y.; Shen, W. F., Molecular Dynamics Simulation Study of the Structural Characteristics of Water Molecules Confined in Functionalized Carbon Nanotubes. J. Phys. Chem. B, 2006, 110 (51): 25761-25768.

(41) Huang, L. L.; Shao, Q.; Lu, L. H.; Lu, X. H.; Zhang, L. Z.; Wang, J.; Jiang, S. Y., Helicity and Temperature Effects on Static Properties of Water Molecules Confined in Modified Carbon Nanotubes. Phys. Chem. Chem. Phys. 2006, 8 (33): 3836-3844.