GUEST POST: Prof. Vincent Voelz, Temple University
The Voelz Lab just started this past August in the Department of Chemistry at Temple University in Philadelphia, PA. We have just installed two Folding@home servers, and are gearing up to run simulations this summer (which I hope to talk about in future blog posts). In the meantime we have been very lucky to work with the Institute for Computational Molecular Science here at Temple, and a new high-peformance computing cluster to generate some initial data.
One of our interests is using molecular simulation to do computational design of folding and binding properties. Design efforts require looking at folding for lots of different possible protein sequences, which is a natural task for a distributed computing platform like Folding@home. We're working on ways to leverage Markov State Models of conformational dynamics to do efficient estimation of the effects of sequence perturbations. A good starting point to test these ideas are to look at proteins for which many sequences have been characterized, to see if we can predict sequence-dependent changes. Many of these sequence mutations are important in human diseases, so we hope to gain insight into these process as well.