Nucleic Acids

My first scientific project dealt with a DNA minor-groove binder. I was a bachelor student, a fresh member of Pavel's group, and I didn't know any single bash command. Since then, I've 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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