Lawrence Livermore National Laboratory
Ph.D.: Computational Chemistry - University of California, Santa Barbara - 2007
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.
- X. Zhang, H. Péréz-Sánchez, and F. C. Lightstone. (2015) Molecular Dynamics Simulations of Ligand Recognition Upon Binding Antithrombin: A MM/GBSA Approach. Bioinformatics and Biomedical Engineering, 9044, 584-593.
- M. X. LaBute, X. Zhang, J. Lenderman, B. J. Bennion, S. E. Wong, F. C. Lightstone (2014) Adverse Drug Reaction Prediction Using Scores Produced by Large-Scale Drug-Protein Target Docking on High-Performance Computing Machines. PLoS ONE, 9(9): e106298.
- X. Zhang, S. E. Wong, F. 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(1) 324-337.
- X. Zhang, S. E. Wong, F. 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.
- R. Custelcean, P. V. Bonnesen, N. C. Duncan, X. Zhang, L. A. Watson, G. Van Berkel, W. B. Parson, and B. 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.
- J. Nadas, X. Zhang, and B. P. Hay. (2011) Shapes of Sulfur, Oxygen, and Nitrogen Mustards, J. Phys. Chem. A 115, 6709-6716.
- X. Zhang, A. C. Gibbs, C. H. Reynolds, M. B. Peters, and L. M. Westerhoff. (2010) Quantum Mechanical Pairwise Decomposition Analysis of Protein Kinase B Inhibitors: Validating a New Tool for Guiding Drug Design, J. Chem. Inf. Model. 50, 651-661.
- D. J. Diller, C. Humblet, X. Zhang, and L. M. Westerhoff. (2010) Computational alanine scanning with linear scaling semiempirical quantum mechanical methods, Proteins-Struct. Funct. Bioinf. 78, 2329-2337.
- X. Zhang, and T. C. Bruice. (2008) Complexation of single strand telomere and telomerase RNA template polyanions by deoxyribonucleic guanidine (DNG) polycations: Plausible anticancer agents, Biorg. Med. Chem. Lett. 18, 665-669.
- X. Zhang, and T. C. Bruice. (2007) Diels-Alder ribozyme catalysis: A computational approach, J. Am. Chem. Soc. 129, 1001-1007.
- X. Zhang, and T. C. Bruice. (2007) Temperature-dependent structure of the ES complex of Bacillus stearothermophilus alcohol dehydrogenase, Biochemistry. 46, 837-843.
- X. Zhang, and T. C. Bruice. (2006) Temperature dependence of the structure of the substrate and active site of the Thermus thermophilus chorismate mutase ES complex, Biochemistry. 45, 8562-8567.
- X. Zhang, and T. 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
- X. D. Zhang, X. Zhang, and T. C. Bruice. (2005) A definitive mechanism for chorismate mutase, Biochemistry. 44, 10443-10448.
- D. F. Liu, A. B. Seuthe, O. T. Ehrler, X. Zhang, T. Wyttenbach, J. F. Hsu, and M. T. Bowers. (2005) Oxytocin-receptor binding: Why divalent metals are essential, J. Am. Chem. Soc. 127, 2024-2025.