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

ConveyorLC

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

Jonathan P. Cranford, Thomas J. O’Hara, Christopher T. Villongco, Omar M. Hafez, Robert C. Blake, Joseph Loscalzo, Jean–Luc Fattebert, David F. Richards, Xiaohua Zhang, James N. Glosli, Andrew D. McCulloch, David E. Krummen, Felice C. Lightstone, and Sergio E. Wong. (2018) Efficient computational modeling of human ventricular activation and its electrocardiographic representation: A sensitivity study. Cardiovascular Engineering and Technology, 9, 447–467.

X. Zhang, H. Péréz-Sánchez, and F. C. Lightstone. (2017) A Comprehensive Docking and MM/GBSA Rescoring Study of Ligand Recognition upon Binding Antithrombin. Current Topics in Medicinal Chemistry, 17, 1-9.

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.