(Bio)molecular Dynamics

All molecules are dynamic and even at absolute zero temperature, there is some motion preserved due to Heisenberg's uncertainty principle. The larger a molecules is, the more functionally important its motion can be and this is especially true about biomolecules. They move like Jagger. We study their choreography to understand what the biomolecules do, how they are regulated and what one can do to modulate their function to e.g. cure a dissease.

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Nucleic Acids

The first scientific project of Michal dealt with a DNA minor-groove binder. He was a bachelor student, a fresh member of Pavel's group, and He didn't know any single bash command. Since then, he's studied the DNA double-helix, a piece of HIV-1 untranslated mRNA, and the ribosome.

Ribosome anatomy

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Halogen Bonding

The halogen bond is a kind of non-covalent interaction, which involves a halogen atom (e.g. bromine) and a Lewis base (e.g. carbonyl oxygen). It means that if these two guys attract each other, we can speak about a halogen bond between them. There are two major areas, where the interest in halogen bonding has been growing terribly fast: crystal engineering and drug design.

Prototypical halogen bond

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Sigma-Holes

Sigma-holes were discovered (slash described?) in 1992, but at that time nobody called them sigma-holes. The term appeared for the first time in the seminal paper of Tim Clark and coworkers. Interestingly, my Alma mater in Prague played some role in the whole story. Sigma-holes provide an elegant explanation of some (actually many of) halogen bonding features.

Sigma-Hole

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Quantum-Chemical Scoring

In computer-aided drug design, the scoring is an important technique to assess the quality of drug candidates. Often it is based on knowledge of the atomistic structure of the drug-receptor complex. A typical task is to test a lot of drug candidates, scoring must be computationally fast and reliable at the same time. Folks in the lab of Pavel Hobza work on scoring which involves quantum chemical calculations and since my Ph.D. I've had a chance to contribute a bit.

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