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Samuel Demharter

Samuel Demharter

Doctoral Student

Leaving date: 15th August 2017

Interests

Novel Applications for Natural Move Monte Carlo Simulations: From Protein Complexes to Nanomachines

My research revolves around the sampling of structural conformations of protein complexes and molecular machines. For this purpose I use the MOSAICS software package (Minary 2007) to perform Hierarchical Natural Move Monte Carlo simulations (Sim 2012). This method makes use of a combination of complexity reducing concepts with the aim to make molecular modeling of large complexes and their structural changes tractable. Key features include multicanonical sampling protocols, 3pt representation and the use of knowledge potentials (Minary 2008). In addition we decompose our structures into groups of residues that are known or expected to move in concert "naturally". Sampling along these pre-defined degrees of freedom results in an ensemble of structures that can be represented by probability distributions that describe the "event space". Clustering of the structures subequently provides us with possible candidates for alternative conformers.

Current work revolves around functional motions in MHC complexes as well as the impact of epigenetic marks on nucleic acid structures. 

References:
Minary, P., 2007. MOSAICS versions [-3.9]. Available at: http://www.cs.ox.ac.uk/mosaics.
Minary, P. & Levitt, M., 2008. Probing protein fold space with a simplified model. Journal of molecular biology, 375(4), pp.920–33.
Sim, A.Y.L., Levitt, M. & Minary, P., 2012. Modeling and design by hierarchical natural moves. Proceedings of the National Academy of Sciences of the United States of America, 109(8), pp.2890−5.

 

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