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Department of Biochemistry & Molecular Biology, Baylor College of Medicine

The projects in our research group aim at the frontier of modern computational biophysics and structural biology. There are three major research directions:

• Molecular Dynamics (MD) Simulation of Supermolecular Complexes
  Large-scale conformational transitions in protein structures play an important role in a variety of cellular processes. Understanding such transitions is one of the central tasks of modern biophysics and structural biology. Among all the available structural and biophysical methods, computer simulation is a powerful method that allows one to model the motions of proteins in atomic details.
  
  The research projects primarily focus on systems that involve coordinated large domain movements. Our recent work on the molecular chaperonin GroEL provided a paradigm for this type of research, and it also demonstrates that molecular dynamics simulation has come into an age of realistically modeling very large protein complexes.
  
• Structural Refinement for X-ray Crystallography and EM Reconstruction
  In recent history, application of molecular dynamics simulation has significantly improved the structural refinement in x-ray crystallography. However, as structural biology moves towards new challenges from systems such as motors in which parts of the structures are inherently mobile, it is increasingly important to employ more advanced computational methods to model such motions in structure refinement.
  
  Another important trend in structural biology is the fast development of Electron Microscopy (EM) reconstruction, which is now able to deliver 6-7 E resolution for systems that are difficult to handle by conventional NMR and x-ray crystallography. A combination of EM reconstruction and computational modeling harbors the hope for future realization of atomic resolution measurement. Our goal is to use and develop the state-of-the-art simulation methods to meet the demand of frontier experimental measurement.
  
• Computer-Aided Drug-Design
  As a part of bioinformatics, computer-aided drug design has been an exploding field in recent years.
  
  The research of our group will use both the structure-based approaches and ligand-based approaches such as QSAR (Quantitative Structure-Function Relationship) methods. Several important systems are being targeted.