The interactions between proteins, DNA and small ligands among others are behind all the functionality in living organisms. I work with computational models that allow us to rationalize how these interactions happen, how we can inhibit them or promote them.
We are currently working on a protocol to reduce the cost of determining protein structures by combining sparse experimental data with computational tools. We make use of hamiltonian replica exchange molecular dynamics and GPU (graphical processing unit) technology to make sampling more efficient (as opposed to the more traditional use of CPUs).
DNA-protein interactions determine which genes are going to be expressed and which are not. Proteins can “read” certain DNA sequences by establishing certain interactions. However, DNA also plays a role, different sequences are able to deform to conformations that allow protein-DNA interactions and some cannot (indirect readout). I study this sequence dependent properties to predict functional parts of the genome.