Samuel Demharter

PhD student in the Department of Computer Science
Computational Biology Group & Oxford Protein Informatics Group
University of Oxford

Structural changes in biomolecules.

In the Minary group we study functional motions in protein and DNA structures using statistical sampling techniques. One of our tools is Natural Move Monte Carlo (NMMC): A highly efficient conformational sampling method that uses generalised coordinates to approximate motions in macromolecular structures. In a recent study (Moraga et al.) we applied this method to investigate the linker flexibility in diabodies that were shown to "tune" cytokine signalling. The movie on the right shows three conformations of a diabody/EPO-receptor complex (DA10/EPO-R) as predicted by NMMC.

Epigenetic marks on DNA and RNA.

Using Natural Moves we are investigating the effects of epigenetic marks on the structure of DNA molecules. A unique feature of this method allows us to customise degrees of freedom to ask questions and test hypotheses.

On the left you can see a short trajectory of a toy simulation (based on Schofield et al., 2014). Given recent advances in solving DNA structures with epigenetic marks and our efficient sampling methods we are hoping to soon gain insights into understanding the structural effects of epigenetic marks on DNA and RNA.

  • 2013-2016: PhD Project at the Department of Computer Science, University of Oxford
    Thesis title: Novel applications for Natural Move Monte Carlo simulations: From small proteins to nanomachines.
  • 2012-2013: Doctoral training at DTC Systems Biology, University of Oxford
  • 2008-2012: BSc Biological Sciences with Industrial Placement, University of Leeds