Book Chapters

• Grant BJ, Skjærven L, and Yao XQ. Comparative protein structure analysis with Bio3D-web. Methods in Molecular Biology (2019), submitted (invited).

Peer Reviewed Journal Articles (*Joint-First, ^#Co-corresponding)

1. Yao XQ^#, Momin M, and Hamelberg D^#. Establishing a Framework of Using Residue-Residue Interactions in Protein Difference Network Analysis. J Chem Inf Model (2019) in press.
2. Li H, Yao XQ, and Grant BJ. Comparative structural dynamic analysis of GTPases. PLoS Comput Biol (2018) 14:e1006364. link
3. Yao XQ^#, Momin M, and Hamelberg D^#. Elucidating allosteric communications in proteins with difference contact network analysis. J Chem Inf Moldel (2018) 58:1325-1330. link
4. Rodriguez-Bussey I, Yao XQ, Shouaib AD, Lopez J, and Hamelberg D. Decoding allosteric communication pathways in cyclophilin A with a comparative analysis of perturbed conformational ensembles. J Phys Chem B (2018) 122:6528-6535. link
5. Momin MF, Yao XQ, Thor W, and Hamelberg D. Substrate sequence determines catalytic activities, domain-binding preferences, and allosteric mechanisms in Pin1. J Phys Chem B (2018) 122:6521-6527. link
6. Vu PJ*, Yao XQ*, Momin M, and Hamelberg D. Unraveling allosteric mechanisms of enzymatic catalysis with an evolutionary analysis of residue-residue contact dynamical changes. ACS Catalysis (2018) 8:2375-2384. link
7. Yao XQ*, Cato MC*, Labudde E, Beyett TS, Tesmer JJG, and Grant BJ. Navigating the conformational landscape of G protein-coupled receptor kinases during allosteric activation. J Biol Chem (2017) 292:16032-16043. link
8. Bouley R, Waldschmidt HV, Cato MC, Cannavo A, Song J, Cheung JY, Yao XQ, Koch WJ, Larsen SD, and Tesmer JJG. Structural determinants influencing the potency and selectivity of indazole-paroxetine hybrid G protein-coupled receptor kinase 2 inhibitors. Mol Pharmacol (2017) 92:707-717. link
9. Stender JD, Nwachukwu JC, Kastrata I, Kim Y, Strid T, Yakir M, Srinivasan S, Nowak J, Izard T, Erumbi R, Carlson KE, Katzenellenbogen JA, Yao XQ, Grant BJ, Leong HS, Lin CY, Frasor J, Nettles KW, Glass C. Structural and molecular mechanisms of cytokine-mediated endocrine resistance in human breast cancer cells. Mol Cell (2017) 65:1122-1135.e5. link
10. Nwachukwu JC, Srinivasan S, Bruno NE, Nowak J, Wright NJ, Minutolo F, Rangarajan ES, Izard T, Yao XQ, Grant BJ, Kojetin DJ, Elemento O, Katzenellenbogen JA, Nettles KW. systems structural biology analysis of ligand effects on ERα predicts cellular response to environmental estrogens and anti-hormone therapies. Cell Chem Biol (2017) 24:35-45. link
11. Jariwala S, Skjærven L, Yao XQ, and Grant BJ. Investigating protein sequence-structure-dynamics relationships with Bio3D-web. J Vis Exp (2017) 125:e55640. link
12. Yao XQ, Skjærven L, and Grant BJ. Rapid characterization of allosteric networks with ensemble normal mode analysis. J Phys Chem B (2016) 120:8276-8288. link
13. Yao XQ*, Malik RU*, Griggs NW, Skjaerven L, Traynor JR, Sivaramakrishnan S, and Grant BJ. Dynamic coupling and allosteric networks in the alpha subunit of heterotrimeric G proteins. J Biol Chem (2016) 291:4742-4753. link
14. Skjærven L, Jariwala S, Yao XQ, and Grant BJ. Online interactive analysis of protein structure ensembles with Bio3D-web. Bioinformatics (2016) 32:3510-3512. link
15. Scarabelli G, Soppina V, Yao XQ, Atherton J, Moores C, Verhey K, and Grant BJ. Mapping the processivity determinants of the kinesin-3 motor domain. Biophys J (2015) 109:1537-1540. link
16. Skjaerven L, Yao XQ, Scarabelli G, and Grant BJ. Integrating protein structural dynamics and evolutionary analysis with Bio3D. BMC Bioinformatics (2014) 15:399. link
17. Yao XQ and Grant BJ. Domain-opening and dynamic coupling in the α-subunit of heterotrimeric G proteins. Biophys J (2013) 105:L08-L10. link
18. Yao XQ, Kimura N, Murakami S, and Takada S. Drug uptake pathways of multidrug transporter AcrB studied by molecular simulations and site-directed mutagenesis experiments. J Am Chem Soc (2013) 135:7474-7485. link
19. Kenzaki H, Koga N, Hori N, Kanada R, Li WF, Okazaki K, Yao XQ, and Takada S. CafeMol: a coarse-grained biomolecular simulator for simulating proteins at work. J Chem Theory Comput (2011) 7:1979-1989. link
20. Yao XQ, Kenzaki H, Murakami S, and Takada S. Drug export and allosteric coupling in a multidrug transporter revealed by molecular simulations. Nature Commun (2010) 1:117. (The work was reported by public media: Nikkei Business Daily, Nikkan Kogyo Shimbun, and Kyoto Shimbun). link
21. Gao M, Zhu HQ, Yao XQ, and She ZS. Water dynamics clue to key residues in protein folding. Biochem Biophys Res Comm (2010) 392:95-99. link
22. Gao M, Yao XQ, She ZS, Liu ZR, and Zhu HQ. Intermediate structure and slow hydration water dynamics in protein folding process. Acta Physico-chimica Sinica (2010) 26:1998-2006. link
23. Kang H, Yao XQ, She ZS, and Zhu HQ. Water-protein interplay reveals the specificity of alpha-lytic protease. Biochem Biophys Res Comm (2009) 385:165-169. link
24. Yao XQ and She ZS. Key residue-dominated protein folding dynamics. Biochem Biophys Res Comm (2008) 373:64-68. link
25. Yao XQ, Zhu HQ, and She ZS. A dynamic Bayesian network approach to protein secondary structure prediction. BMC Bioinformatics (2008) 9:49. link

Talks

• “Elucidating allosteric communications in proteins with difference contact network analysis”, The 256th ACS National Meeting & Exposition, Boston (2018)
• “Allosteric modulation of G protein-coupled receptor kinase (GRK) activation,” Sigtrans Seminar, University of Michigan (2017)
• “Dynamic coupling and activation mechanisms of heterotrimeric G proteins,” (2016) Cytoskeleton Seminar, University of Michigan
• “Dynamic coupling and allosteric networks in the alpha subunit of heterotrimeric G proteins,” (2015) Sigtrans Seminar, University of Michigan
• “G protein allosteric networks from molecular dynamics and normal mode analysis,” (2014) Sigtrans Seminar, University of Michigan
• “Probing the activation mechanism of heterotrimeric G proteins with multiscale molecular simulations,” (2014) Tools and Technology Seminar, University of Michigan
• “Nucleotide-dependent Transitions of the alpha-subunit of heterotrimeric G proteins probed with computational methods,” (2013) Sigtrans Seminar, University of Michigan
• “Drug translocation and allosteric coupling in a multidrug transporter studied by molecular simulations,” (2011) The 17th International Biophysics Congress (IUPAC), Beijing, China
• “Functionally rotating mechanism of a multidrug transporter studied by coarse-grained simulations,” (2011) The 13th Annual Meeting of Chinese Life Science Association, Kyoto, Japan
• “The uptake and export of drugs in a multidrug transporter studied by coarse-grained simulations,” (2011) The 49th Annual Meeting of the Biophysical Society of Japan, Himeji, Japan
• “Drug export and allosteric coupling in a multidrug transporter revealed by molecular simulations,” (2011) New Era of Biosimulations with Supercomputers, Osaka, Japan
• “Functionally rotating mechanism of a multidrug transporter studied by coarse-grained simulation,” (2010) The 47th Annual Meeting of the Biophysical Society of Japan, Tokushima, Japan
• “Rotatory mechanism of AcrB transporter studied by coarse-grained simulation,” (2009) Workshop for Next-Generation Integrated Simulation of Living Matters on Molecular Scale, Tokyo, Japan
• “Protein sequence, structure, and dynamics,” (2007) Institute for theoretical physics, Chinese Academy of Science, Beijing, China

Posters

• Vu PJ, Yao XQ, Momin M, and Hamelberg D. Evolutionarily conserved and divergent residue-residue contact dynamics provide insights into the allosteric regulation of cyclophilins. The 9th Southeast Enzyme Conference, Atlanta (2018)
• Vu PJ, Yao XQ, Momin M, and Hamelberg D. Evolutionarily conserved and divergent residue-residue contact dynamics provide insights into the allosteric regulation of cyclophilins. The 255th ACS National Meeting & Exposition, New Orleans (2018)
• Vu PJ, Yao XQ, Momin M, and Hamelberg D. Evolutionarily conserved and divergent residue-residue contact dynamics provide insights into the allosteric regulation of cyclophilins. The 62nd Annual Meeting of Biophysical Society, San Francisco (2018)
• Yao XQ, Jariwala S, Grant BJ. In silico prediction of HLA-associated drug hypersensitivity. The 61st Annual Meeting of Biophysical Society, New Orleans (2017)
• Yao XQ, Malik RU, Griggs NW, Skjaerven L, Traynor JR, Sivaramakrishnan S, Grant BJ. Dynamic coupling and allosteric networks in the alpha subunit of heterotrimeric G proteins. (2016) The 60th Annual Meeting of Biophysical Society, LA.
• Skjaerven L, Jariwala S, Yao XQ, Ide J, Grant BJ. The Bio3D project: interactive tools for Structural Bioinformatics. (2016) The 60th Annual Meeting of Biophysical Society, LA.
• Skjaerven L, Yao XQ, Jariwala S, Grant BJ. Bio3D: interactive tools for structural bioinformatics. (2016) The 60th Annual Meeting of Biophysical Society, LA.
• Scarabelli G, Soppina V, Yao XQ, Atherton J, Moores CA, Verhey KJ, Grant BJ. Mapping the processivity determinants of the kinesin-3 motor domain. (2016) The 60th Annual Meeting of Biophysical Society, LA.
• Li H, Yao XQ, Grant BJ. Comparative structure dynamic analysis of G proteins. (2016) The 60th Annual Meeting of Biophysical Society, LA.
• Yao XQ, Skjaerven L, Grant BJ. Characterizing nucleotide dependent allostery in G-proteins with molecular dynamics and normal mode analysis. (2015) Symposium on Computational Discovery in Complex Systems Biology, University of Michigan.
• Yao XQ, Skjaerven L, and Grant BJ. G-protein allosteric networks from molecular dynamics and normal mode analysis (2015) The 59th Annual Meeting of Biophysical Society, Baltimore
• Yao XQ, Scarabelli G, Skjaerven L, Grant BJ. The Bio3D package: new interactive tools for Structural Bioinformatics. (2014) The 58th Annual Meeting of Biophysical Society, San Francisco
• Yao XQ, Jariwala S, and Grant BJ. Predicting HLA-specific drug hypersensitivity with molecular docking and molecular dynamics simulation. (2014) The 58th Annual Meeting of Biophysical Society, San Francisco
• Yao XQ and Grant BJ. Nucleotide-dependent transitions of the alpha subunit of heterotrimeric G-proteins probed with accelerated molecular dynamics simulations. (2013) The 57th Annual Meeting of Biophysical Society, Philadelphia
• Yao XQ, Kenzaki H, and Takada S. Functionally rotating mechanism of a multidrug transporter studied by coarse-grained simulation: exploring the binding pathways of drugs. (2011) The 55th Annual Meeting of Biophysical Society, Baltimore
• Yao XQ, Kenzaki H, and Takada S. Functionally rotating mechanism of a multidrug transporter studied by coarse-grained simulations. (2010) The 54th Annual Meeting of the Biophysical Society, San Francisco
• Kenzaki H, Koga N, Fujiwara S, Hori N, Kanada R, Okazaki K, Yao XQ, Li WF, Takada S. Biomolecular coarse-grained simulation program CafeMol. (2010) The 54th Annual Meeting of the Biophysical Society, San Francisco
• Yao XQ, Kenzaki H, and Takada S. Functionally rotating mechanism of multidrug transporter studied by coarse-grained simulations. (2010) The 48th Annual Meeting of the Biophysical Society of Japan, Sendai, Japan
• Yao XQ, Kenzaki H, and Takada S. Functionally rotating mechanism of a multidrug transporter studied by coarse-grained simulation. (2010) The 2nd Biosupercomputing Symposium, Tokyo, Japan
• Yao XQ, Kenzaki H, and Takada S. Functionally rotating mechanism of a multidrug transporter studied by coarse-grained simulation. (2010) The 4th International Symposium on Molecular Science of Fluctuations toward Biological Functions, Shiga, Japan