Research

My primary research interests lie in bioinformatics and computational biology. More specifically, I am interested in structural genomics and systems biology, protein structure determination, and protein and drug design.

  1. NMR Assignment, Protein Structure Determination and Structural Genomics

    2. In collaboration with members of Prof. Bruce Donald's and Prof. Pei Zhou's Labs, I have developed two open-source software packages, NASCA and RDCPANDA, for automated NMR assignment and high-resolution protein structure determination. NASCA performs side-chain resonance and NOE assignments without requiring TOCSY-type experiments, and thus can relieve the current bottleneck in NMR structure determination for large proteins. RDC-PANDA is a novel approach that exploits the global orientational restraints from sparse residual dipolar coupling (RDC) data to filter ambiguous NOE assignments, and can be used for high-resolution structure determination.

  2. Protein Design

    3. I am also interested in the protein design field. My research has integrated protein design algorithms into side-chain resonance assignment and rotamer optimization with unassigned NOE data. My research has also developed a Bayesian inference approach to compute an optimal pseudo-energy function for protein structure modelling. This Bayesian approach can be extended to improve the accuracy of the energy function employed in protein design.

  3. Antibody Structure Modelling and Computational Prediction of Receptor-Ligand Interactions

    4. I am also interested in applying computational techniques to study the anti-glomerular basement membrane (GBM) nephritis, an autoimmune kidney disease. Currently, little is known about the pathogenic mechanism of anti-GBM disease. Recent studies on immune tolerance have indicated the existence of a second unsuspected self antigen that regulates the development of anti-GBM B cells. Identification of this unknown self antigen and elucidation of B cell receptor-ligand interactions will provide new insights into understanding the pathogenesis of anti-GBM disease, and broaden the diagnostic and therapeutic methods. My research goal is to apply in silico techniques to predict the second self antigen that engages in the nephritogenic reactivity of anti-GBM disease and explore the molecular basis of receptor-ligand interactions for studying human autoimmunity and pathogenic pathways. This project is joint work between Prof. Bruce Donald's and Prof. Mary Foster's Labs.