Yuhua Song Research Group
An Integrated Multiscale Computational Modeling and Experimental Research Program
1. Biologically Active Vitamin D and Lumisterol Derivatives Act on Liver X Receptors (LXRs). Scientific Reports. Slominski et al. 2021; 11: 8002, doi:10.1038/s41598-021-87061-w.
2. Functional insights from biophysical study of TREM2 interactions with ApoE and Ab1-42. Featured Article, Alzheimer’s and Dementia,Kober et al. 2020, Online ahead of print, Oct 8, 2020, https://doi.org/10.1002/alz.12194
3. Photoprotective properties of vitamin D and lumisterol hydroxyderivatives. Cell Biochemistry and Biophysics, Slominski etc. 2020. 78(2): p. 165-180, https://doi.org/10.1007/s12013-020-00913-6
4. Molecular Insight for the Role of Key Residues of Calreticulin in its Binding Activities: A Computational Study. Computational Biology and Chemistry, Yang et al. [In press, published online ahead of print, February 3, 2020] https://doi.org/10.1016/j.compbiolchem.2020.107228.
5. Molecular insights into the effect of an apoptotic raft-like bilayer on the conformation and dynamics of calreticulin. Biochimica et Biophysica Acta (BBA) – Biomembranes. Wang et al. 2020,1862(2): p. 183146. [In press, published online ahead of print, December 6, 2019]. https://doi.org/10.1016/j.bbamem.2019.183146
6. Neurodegenerative Disease–Associated Variants in TREM2 Destabilize the Apical Ligand-Binding Region of the Immunoglobulin Domain. Frontiers in Neurology, Dean et al. 2019, 10(1252). Published on November 26, 2019. doi: 10.3389/fneur.2019.01252
7. Multiscale Simulation of the Interaction of Calreticulin-Thrombospondin-1 Complex with a Model Membrane Microdomain. J Biomol Struct Dyn., Wang et al. 2019, 37(3):811-822. doi: 10.1080/07391102.2018.1433065.
8. Calmodulin antagonist enhances DR5-mediated apoptotic signaling in TRA-8 resistant triple negative breast cancer cells. J Cell Biochem. Fancy et al. published:16 April 2018, https://doi.org/10.1002/jcb.26848
9. Activation Mechanisms of αVβ3 Integrin by Binding to Fibronectin: A Computational Study. Protein Science, Wang et al. 2017, June; 26(6):1124-1137. DOI:10.1002/pro.3163
10. Calmodulin Binding to Death Receptor 5-mediated Death-inducing Signaling Complex in Breast Cancer Cells. J Cell Biochem. Fancy et al. 2017 Aug;118(8):2285-2294. doi: 10.1002/jcb.25882. Epub 2017 Apr 12.
11. Characterization of the Interactions between Calmodulin and Death Receptor 5 in Triple-Negative and Estrogen Receptor Positive Breast Cancer Cells: An Integrated Experimental and Computational Study. J Biol Chem. Fancy et al, 2016, 291:12862-12870
12. Structural insight for roles of DR5 death domain mutations on oligomerization of DR5 death domain – FADD complex in the death-inducing signaling complex formation: a computational study. Journal of Molecular Modeling, Yang et al. 2016, 22 (4):89.
13. Molecular insight for the effect of lipid bilayer environments on thrombospondin-1 and calreticulin interactions. Biochemistry, Liu et al., 2014, 53(40):6309-22;
15. Structural Insight for the Roles of Fas Death Domain Binding to FADD and Oligomerization Degree of the Fas – FADD complex in the Death Inducing Signaling Complex Formation: A Computational Study.Proteins: Structure, Function, and Bioinformatic, Yan et al., 2013, 81(3):377-85;
16. Effects of altered restraints in β1 integrin on the force-regulated interaction between the glycosylated I-like domain of β1 integrin and fibronectin III9-10: a steered molecular dynamic study.Molecular & Cellular Biomechanics, Pan et al., 2011, 8(3): 233-52;
20. Role of Altered Sialylation of the I-like Domain of β1 Integrin in the Binding of Fibronectin to β1 Integrin: Thermodynamics and Conformational Analyses. Biophys J, Pan et al., 2010, 99 (1): 208-217;
22. Amiloride Docking to Acid-sensing Ion Channel-1. Journal of Biological Chemistry, Qadri et al., 2010, 285(13): 9627-9635.
23. Psalmotoxin-1 docking to human acid sensing ion channel-1. Journal of Biological Chemistry, Qadri et al., 2009, 284(26): 17625-17633;
25. Effect of Altered Glycosylation on the Structure of the I-like Domain of beta1 Integrin: A Molecular Dynamics Study. Proteins: Structure, Function, and Bioinformatic, Liu et al., 2008, 73(4): 989-1000;
27. Molecular dynamics simulations of asymmetric NaCl and KCl solutions separated by phosphatidylcholine bilayers: potential drops and structural changes induced by strong Na+-lipid interactions and finite size effects. Biophys J, Lee et al.,2008, 94(9): 3565-3576;
28. D-Periodic Collagen-Mimetic Microfibers. J Am Chem Soc., Rele et al., 2007, 129(47): 14780-14787;
30. Molecular dynamics simulation of salicylate effects on the micro- and mesoscopic properties of a dipalmitoylphosphatidylcholine bilayer.Biochemistry, Song et al., 2005, 44(41), 13425-13438;
31. Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state smoluchowski equation using finite element methods.Biophys. J, Zhang et al., 2005, 88(3):1659-1665;
32. Continuum diffusion reaction rate calculations of wild type and mutant mouse acetylcholinesterase: adaptive finite element analysis.Biophys. J, Song et al., 2004, 87(3):1558-1566;
34. Three Dimensional Finite Element Model of the Human Anterior Cruciate Ligament – A Computational Analysis with Experimental Validation. J Biomech., Song et al., 2004, 37(3):383-390
Department of Biomedical Engineering The University of Alabama at Birmingham
35. In silico identification of available drugs targeting cell surface BiP to disrupt SARS-CoV-2 binding and replication: Drug repurposing approach. Journal of Pharmaceutical Sciences. Zhang et al. 2021:105771. Online ahead of print, doi: https://doi.org/10.1016/j.ejps.2021.105771