Computational & Experimental
Structural Biology & Cell Biology
Dr. Jianpeng Ma
Baylor College of Medicine & Rice University, Houston, Texas
 
New & Notable
Available Positions
 
Multi-resolution and Multi-length Scale Simulation of Supermolecular Complexes

In recent history, molecular dynamics simulation has been successfully employed to significantly improve the structure refinement in x-ray crystallography. However, as structural biology moves towards meeting the new challenges imposed by the study of more complex and more dynamic biological systems, more advanced computational methods are urgently needed to effectively deal with molecular motions in structure refinement. 

Our group is committed to improving structure refinement in X-ray crystallography, electron cryomicroscopy (cryo-EM) and fiber diffraction. QEDM has been demonstrated highly effective in assisting cryo-EM single-particle reconstruction of intrinsically flexible biological systems. SSM is extremely powerful for enhancing the structure refinement against fiber diffraction data. Moreover, important progress of improving x-ray structure refinement has been recently achieved. These lines of research will undoubtedly provide powerful tools for structure refinement in the wider fields of structural biology.

Structural Refinement for X-ray, cryo-EM and Fiber Diffraction

In recent history, molecular dynamics simulation has been successfully employed to significantly improve the structure refinement in X-ray crystallography. However, as structural biology moves towards meeting the new challenges imposed by the study of more complex and more dynamic biological systems, more advanced computational methods are urgently needed to effectively deal with molecular motions in structure refinement. 

Our group is committed to improving structure refinement in X-ray crystallography, electron cryomicroscopy (cryo-EM) and fiber diffraction. Quantized elastic deformational model (QEDM) has been demonstrated highly effective in assisting cryo-EM single-particle reconstruction of intrinsically flexible biological systems. Substructure synthesis method (SSM) is extremely powerful for enhancing the structure refinement against fiber diffraction data. Moreover, important progress of improving X-ray structure refinement has been recently achieved. These lines of research will undoubtedly provide powerful tools for structure refinement in the wider fields of structural biology.

Structure Modeling and Prediction

With the advance of cryo-EM single-particle reconstruction, more and more intermediate-resolution structures are available. It would be extremely useful if protein secondary structures and protein topology can be determined from intermediate-resolution data.

Our group has recently developed sheetminer and sheettracer that are capable of accurately locating beta-sheets and building beta-strands in intermediate-resolution density maps. Once protein secondary structures are in place, protein topology can be determined using approaches developed in our group. These methods will greatly enhance one's ability to obtain meaningful information about protein structure and function from intermediate-resolution data.

 
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last updated Dec. 10, 2007