Welcome

I am a Research Associate at the University of Pittsburgh. My research interests include understanding the principles of protein-drug interactions and discovery of small-molecule inhibitors for challenging target proteins, such as MAP kinase phosphatases and cytochome c.

Protein Dynamics

Dynamics plays an important role in protein function and recognition. Heterogeneous structural ensembles of target proteins in the PDB is a rich resource for understanding the role of dynamics in drug binding. I have designed and developed a Python software, ProDy, for efficient analysis of large datasets. We used ProDy to study the role of dynamics in protein-drug binding. The movie shows functional motions of HIV reverse transcriptase inferred from experiments and theory using ProDy. Animation and depictions were generated using NMWiz and movie was made using VMD. References: Bakan et al., Bioinformatics, 2011 ... Bakan and Bahar, Pacific Symposium on Biocomputing, 2011 ... Bakan and Bahar, PNAS, 2011 ...

Protein Druggability

Druggability is an important concept in drug-discovery. Accurate assessment of druggablity allows for making informed decisions on the risk of investing in a particular target. We developed a simulation based method that can identify active sites and allosteric pockets of drug targets and give an estimate of the druggability in terms of maximal achievable affinity. The movie shows a simulation performed for Eg5 kinesin. See how probe molecules identify and induce changes in the binding pocket distinguised by the green flexible loop. We apply this method to MAP kinase phosphatases and cytochome c for identification of new druggable pockets and discovery of small-molecule inhibitors. Read more in our recent paper: Bakan et al., J Chem Theory Comput, 2011