Group Publications

    1. Malik F. and Li Z. Is there a common allosteric binding site for G-protein coupled receptors? J. Computer-Aided Mol. Des. (2022) In press.

    2. Redij T., McKee J.A., Do P., Campbell J. A., Ma J., Li Z., Miller N., Srikanlaya C., Zhang D., Hua X., Li Z. 2-Aminothiophene derivatives as a new class of positive allosteric modulators of glucagon-like peptide 1 receptor. Chemical Biology and Drug Design. (2022) 99(6): 857-867.

    3. Malik F. and Li Z. Non-peptide agonists and positive allosteric modulators of glucagon-like peptide-1 receptor: alternative approaches for treatment of type 2 diabetes. British J. Pharmacology. (2022) 179: 511-525.

    4. Regan K., Saghafi A., Li Z. Splice junction identification using long short-term memory neural networks. Current Genomics. (2021) 22(5): 384-390.

    5. Dang Z., Zhu L., Xie L., Lee K.-H., Malik F., Li Z., Huang L., Chen C-H. Design and synthesis of quinolizidine derivatives as influenza virus and HIV-1 Inhibitors. Current Med. Chem. (2021) 28(24): 4995-5003. PMID: 33372864.

    6. Redij T., Ma J., Li Z., Hua X., Li Z.Discovery of a potential positive allosteric modulator of glucagon-like peptide 1 receptor through virtual screening and experimental study. J. Computer-Aided Mol. Des. (2019) 33: 973-981. PMID: 31758355.

    7. Gunderwala A., Nimbvikar A., Cope N., Li Z., Wang Z. Development of allosteric braf peptide inhibitors targeting the dimer interface of BRAF. ACS Chemical Biology (2019) 14: 1481-1489.

    8. Redij T., Chaudhari R., Li, Z., Hua X., Li Z. Structural Modeling and In SilicoScreening of Potential Small Molecule Allosteric Agonists of Glucagon-Like Peptide 1 Receptor. ACS Omega (2019) 4: 961-970.

    9. Mao B., Gao M., Chen C., Li Z., Zhang H.-Y., Zhang Q.. Design, synthesis and biological evaluation of novel N-nitrophenyl derivatives based on the structure of acetohydroxyacid synthase. Pesticide Biochemistry and Physiology (2018) 145: 100-107. PMID: 29482725.

    10. Dang Z., Xie H., Zhu L., Zhang Q., Li Z., Huang L., Chen C.-H. Structure Optimization of Aloperine Derivatives as HIV-1 Entry Inhibitors. ACS Medicinal Chemistry Letters (2017) 8: 1199-1203.

    11. Yuan X, Yang M, Chen X, Zhang X, Sukhadia S, Musolino N, Bao H, Chen T, Xu C, Wang Q, Santoro S, Ricklin D, Hu J, Lin R, Yang W, Li Z, Qin W, Zhao A. Characterization of the first fully human anti-TEM1 scFv in models of solid tumor imaging and immunotoxin-based therapy. Cancer Immunol. Immunother. (2017) 66(3): 367-378. Note: The modeling figure from this publication showing the binding of scFv78 to human and murine TEM1, was featured on the cover of this issue of the Journal.

    12. Dong D., Xia G., Li Z., Li Z. Human serum albumin and her2-binding affibody fusion proteins for targeted delivery of fatty acid-modified molecules and therapy. Mol. Pharmacology (2016) 13(10): 3370-3380.

    13. Chaudhari R. and Li Z. PyMine: a PyMOL plugin to integrate and visualize data for drug discovery. BMC Research Notes (2015) 8: 517 DOI: 10.1186/s13104-015-1483-3.

    14. Chaudhari R., Heim A. J., and Li Z. Improving homology modeling of G-protein coupled receptors through multiple-template derived conserved inter-residue interactions. J. Computer-Aided Mol. Des. (2015) 29: 413-420.

    15. Rogers B., Dong D., Li Z., and Li Z. Recombinant human serum albumin fusion proteins and novel applications in drug delivery and therapy. Curr Pharm Des. (2015) 21(14): 1899-1907.

    16. Menezes M.J., Guo Y., Zhang J., Riley L.G., Cooper S.T., Thorburn D.R., Li J., Dong D., Li Z., Glessner J., Davis R.L., Sue C.M., Alexander S.I., Arbuckle S., Kirwan P., Keating B.J., Xu X., Hakonarson H., and Christodoulou J. Mutation in mitochondrial ribosomal protein S7 (MRPS7) causes congenital sensorineural deafness, progressive hepatic and renal failure and lactic acidemia. Hum. Mol. Genet. (2015) 24: 2297-2307.

    17. Kufareva, V. Katritch, participants of GPCR Dock 2013 (Box 1), R. C. Stevens, and R. Abagyan, Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges. Structure (2014) 22: 1120-1139.

    18. S. Chaudhuri, S. Pratap, V. Paromov, Z. Li, and H. Xie. Identification of a diguanylate cyclase and its role in porphyromonas gingivalis virulence. Infection and Immunity (2014) 82(7): 2728-2735.

    19. A.J. Heim and Z. Li, Developing a high-quality scoring function for membrane protein structures based on specific inter-residue interactions. J. Computer-Aided Mol. Des. (2012) 26: 301-309.

    20. J. Gao, Z. Li, T. Russell, and Z. Li, Antibody affinity purification using metallic nickel particles. J. Chromatography B (2012) 895–896: 89–93.

    21. V. Pabuwal and Z. Li, Comparison analysis of primary ligand binding sites in seven-helix membrane proteins. Biopolymers (2011) 95: 31-38.

    22. J. Gao and Z. Li, Uncover the conserved property underlying sequence-distant and structure-similar proteins. Biopolymers (2010) 93: 340-347.

    23. J. Gao and Z. Li, Conserved network properties of helical membrane protein structures and its implication for improving membrane protein homology modeling at the twilight zone. J. Computer-Aided Mol. Des. (2009) 23: 755-763.

    24. U. K. Muppirala, S. Desensi, T. P. Lybrand, G. L. Hazelbauer and Z. Li, Molecular modeling of flexible arm-mediated interactions between a bacterial chemoreceptor and its modification enzyme. Protein Sci. (2009) 18: 1702-1714.

    25. J. Gao and Z. Li, Comparing four different approaches for the determination of inter-residue interactions provides insight for the structure prediction of helical membrane proteins. Biopolymers (2009) 91: 547-556.

    26. V. Pabuwal and Z. Li, Comparative analysis of the packing topology of structurally important residues in helical membrane and soluble proteins. Protein Eng. Des. Sel. (2009) 22: 67-73.

    27. J. Gao and Z. Li, Inter-residue interactions in protein structures exhibit power-law behavior Biopolymers (2008) 89: 1174-1178.

    28. J. F. Galan, J. Gao, V. Pabuwal, P. J. Meek and Z. Li, Application of network theory in understanding and predicting protein structure and function. Current Proteomics (2008) 5(3): 181-190.

    29. W. Lai, L. Huang, P. Ho, Z. Li, D. Montefiori and C.-H. Chen, Betulinic Acid Derivatives That Target gp120 and Inhibit Multiple Genetic Subtypes of Human Immunodeficiency Virus Type 1 Antimicrob. Agents Chemother. (2008) 52: 128-136.

    30. V. Pabuwal and Z. Li, Network pattern of residue packing in helical membrane proteins and its application in membrane protein structure prediction. Protein Eng. Des. Sel. (2008) 21: 55-64.

    31. U. K. Muppirala and Z. Li, A simple approach for protein structure discrimination based on the network pattern of conserved hydrophobic residues. Protein Eng. Des. Sel. (2006) 19: 265-275.

Book Chapters

  1. Daoyuan Dong, Z. Li, X. Li, and Z. Li. Recombinant Human Serum Albumin Fusion Proteins: Novel Applications and Challenges. In: Travis Stokes (ed) Human Serum Albumin. Nova Science Publishers. [2015] pp. 47-68.