Biomolecular modeling

Research interests

The Ytreberg lab uses molecular modeling to understand protein function and evolution. Most of our research is done in close collaboration with other scientists who perform experiments on viral and cellular systems.

Ebola, Virus, Protein

Can we predict how protein evolution hampers our ability to treat disease?

Viruses such as Ebola evolve rapidly and can develop amino acid mutations that prevent effective treatment of the disease. We are interested in predicting mutations that could be dangerous to humans by determining which mutations prevent therapeutic molecules from interacting with target proteins.

p53, MDM2, Protein, Affinity

Can we map changes in genes to changes in phenotype?

In order to perform their jobs in cells, most proteins must fold into a well-defined 3D structures and interact with other molecules. We are interested in understanding how amino acid mutations change the ability of proteins to fold and bind, and ultimately how these changes map to higher level phenotypes. See our GenoPheno Project for more on this.

Protein, Binding, Affinity

How well (and quickly) can molecular modeling predict binding affinities?

Methods for calculating binding affinities tend to be based either on rigorous physics principles (accurate, but too slow for many application), or on empirical scoring functions (fast, but not accurate enough for many applications). We are interested in developing methods with a balanced trade-off between speed and accuracy.