Book Chapters

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