Xiaohua Zhang

Contact information

Lawrence Livermore National Laboratory
7000 East Avenue, L-367
Livermore, CA 94550
email: zhang30@llnl.gov
phone: 925 422 2414
        
 

Education

Ph.D.: Computational Chemistry - University of California, Santa Barbara - 2007

Research

I develop novel applications of theoretical/computational chemistry methods and engineer software to implement these methods. My research interests include: (i) drug discovery and high-throughput drug screening C++ toolkit development; (ii) fragment- and structure-based drug design; (iii) high performance computing applied to computational chemistry; (iv) algorithm derivation and program engineering for molecular simulation.

Programs/software

VinaLC

 

Publications

  1. Xiaohua Zhang, Sergio E. Wong, and Felice C. Lightstone. (2014) Toward Fully Automated High Performance Computing Drug Discovery: A Massively Parallel Virtual Screening Pipeline for Docking and Molecular Mechanics/Generalized Born Surface Area Rescoring to Improve Enrichment. J. Chem. Inf. & Model. 54, 324–337
  2. Xiaohua Zhang, Sergio E. Wong, and Felice C. Lightstone. (2013) Message Passing Interface and Multithreading Hybrid for Parallel Molecular Docking of Large Databases on Petascale High Performance Computing Machines. J. Comput. Chem. 34, 915-927.
  3. Radu Custelcean, Peter V. Bonnesen, Nathan C. Duncan, Xiaohua Zhang, Lori A. Watson, Gary Van Berkel, Whitney B. Parson, and Benjamin P. Hay. (2012) Urea-Functionalized M4L6 Cage Receptors: Anion-Templated Self-Assembly and Selective Guest Exchange in Aqueous Solutions. J. Am. Chem. Soc. 134, 8525-8534.
  4. Janos Nadas, Xiaohua Zhang, and Benjamin P. Hay. (2011) Shapes of sulfur, oxygen, and nitrogen mustards. J. Phys. Chem. A. 115, 6709-6716.
  5. Xiaohua Zhang, Alan C. Gibbs, Charles H. Reynolds, and Lance M. Westerhoff. (2010) Quantum mechanical pair-wise decomposition analysis of protein kinase B inhibitors: Validating a new tool for guiding drug design. J. Chem. Inf. & Model. 50, 651-661.
  6. David J. Diller, Christine Humblet, Xiaohua Zhang, and Lance M. Westerhoff. (2010) Computational Alanine Scanning with Linear Scaling Semi-Empirical Quantum Mechanical methods. Proteins: Struct., Funct., Bioinf. 78, 2329-2337.
  7. Xiaohua Zhang, and Thomas C. Bruice. (2008) Complexation of single strand telomere and telomerase RNA template polyanions by deoxyribonucleic guanidine (DNG) polycations: Plausible anticancer agents. Bioorganic & Medicinal Chem. Lett. 18, 665-669.
  8. Xiaohua Zhang, and Thomas C. Bruice. (2007) Diels-Alder ribozyme catalysis: A computational approach. J. Am. Chem. Soc. 129, 1001-1007.
  9. Xiaohua Zhang, and Thomas C. Bruice. (2007) The temperature-dependent structure of the E·S complex of Bacillus stearothermophilus alcohol dehydrogenase. Biochemistry 46, 837-843.
  10. Xiaohua Zhang, and Thomas C. Bruice. (2006) Temperature dependence of the structure of the substrate and active site of the Thermus thermophilus chorismate mutase E·S complex. Biochemistry 45, 8562-8567.
  11. Xiaohua Zhang, and Thomas C. Bruice (2005) The proficiency of a thermophilic chorismate mutase enzyme is solely through an entropic advantage in the enzyme reaction. Proc. Natl. Acad. Sci. U. S. A. 102, 18356-18360.
  12. Xiaodong Zhang, Xiaohua Zhang, and Thomas C. Bruice. (2005) A definitive mechanism for chorismate mutase. Biochemistry 44, 10443-10448.
  13. Dengfeng Liu, Alexandra B. Seuthe, Oli T. Ehrler, Xiaohua Zhang, Thomas Wyttenbach, Jeffrey F. Hsu, and Michael T. Bowers. (2005) Oxytocin-receptor binding: Why divalent metals are essential. J. Am. Chem. Soc. 127, 2024-2025.
  14. Xiaohua Zhang and Zijing Lin. (2003) Coupled thermal and electrochemistry 2D model for solid oxide fuel cell. J. Inorganic Materials 18, 661-666.