Research Interests

Our research is focused on the development of computational methods that combine experimental data with bioinformatics and modeling techniques to characterise the structure of proteins and their assemblies. The structural models are further analysed to understand the dynamics and the effect of mutations on function. Our group is particularly interested in applying these methods using data from cryo electron microscopy and mass spectrometry. In collaboration with experimentalists, systems we currently studies include the Herpes Simplex Virus, the GroEL chaperonin, bacterial secretion systems, glycine transporters and ligand-gated ion channels. 

Selected recent publications

1. •Clare DK et al. (2012) ATP-triggered molecular mechanics of the chaperonin GroEL. Cell (in press).
   

2. •Pandurangan AP and Topf M. Finding rigid bodies in protein structures: Application to flexible fitting into cryoEM maps. J Struct Biol 177:520-531.
   

3. •Vasishtan and Topf (2011) Scoring functions for cryoEM density fitting. J Struct Biol 174:333-343.
   

4. •Zhang et al. (2010) A fast mathematical programming procedure for simultaneous fitting of assembly components into cryo-EM density maps. Bioinformatics 26:i261-8.