National Doctoral Programme in
Informational and Structural Biology

Our group focuses to solve complicated biological problems by using wide variety of molecular modeling techniques. Our aims are to understand the protein structure and dynamics at the atomic level, as well as, discover novel protein subtype selective ligands. Usually the proteins of our interest have significant role in development of diseases. To fully succeed in our aims, we need to employ practically all available tools in computational chemistry and biology. Typically we need to:

• Find all possible information that is available for the target protein, the protein family that binds same/similar ligands and/or have similar function (functional family) and all other proteins with similar fold (structural family)
• Compare the sequences of all members of the structural family
• Model all members of the functional family
• Understand the flexibility of target protein and members of the functional family, both without ligand and with bound ligand
• Use structural differences, caused by differences in amino acid sequence or restrictions in dynamics, inside the protein family to design ligands that bind specifically into target protein

Most of our projects are done in tight collaboration with experimental research groups who work on organic synthesis and/or molecular cell biology. These collaborations allow us to verify our computational predictions in practice and we can put the experimental findings into structural context. In addition, as the current tools that we use are still limited, we participate in software development for the ligand discovery purposes.