Kolář lab at UCT Prague

Tutorial: How to Visualize a Molecular Electrostatic Potential with Molekel

published 2017-08-16

The electrostatic potential is a physical quantity that is valuable for understanding intermolecular interactions such as hydrogen or halogen bonding. It is instructive to project the electrostatic potential onto a molecular surface. Such a visualization, also known as Molecular Electrostatic Potential (MEP), can be done in Molekel 4.3. It is a rather old and not-so-intuitive program with poor documentation, so in this tutorial I decided to describe how to get pictures like this:

Structure and molecular electrostatic potential of bromouracil.
Department Group Photo

Helmut's Department of Theoretical and Computational Biophysics has a brand new group photo.

published 2017-06-30

J. Med. Chem. Perspective

published 2017-06-23

I started studying halogen bonds during my Ph.D. years. I've always been wondering if there are any halogenated ligands known that bind into nucleic acids and form halogen bonds (The Question). Recently, I've analyzed known structures of nucleic acid complexes and with Oriana Tabarrini from University of Perugia we've written a story about the analyses. It's just been accepted as a Miniperspective to The Journal of Medicinal Chemistry (American Chemichal Society). By the way, the answer is No.

Halogen Bonding in Nucleic Acid Complexes

Poly-Glycine in the Tunnel

last update 2017-06-29

The video shows the dynamics of a poly-glycine peptide (in red) in the ribosome exit tunnel as presented on the Hünfeld workshop on computer simulations. A spherical cutout of the ribosome was simulated in Gromacs using facilities in the Leibniz Rechnenzentrum in Munich, Germany.

Simulation time is: 12.50 µs

RNA Society Movies

last update 2017-05-31

Here I publish several videos related to my poster prestention on the 22nd Annual Meeting of the RNA Society in Prague.

Poster Timeline

published 2017-05-28

On the 22nd Annual Meeting of the RNA Society in Prague, I'll present a poster entitled Elongation of the Nascent Peptide in the Ribosomal Exit Tunnel. Feel free to come and discuss on Friday, June 2nd, poster number 659. The video shows, how the poster has evolved from the template about DNA relaxation.

Rubber Stamp

I've just received a rubber stamp.

published 2017-05-20

Emotional Arcs and Random Diffusion

published 2017-05-14

This week I gave a seminar in our group on principal component analysis (PCA). It is a standard computational/mathematical technique to process complex data. During my preparation, I came across an article that uses the PCA to analyze text. The results are somewhat contradicting to what I've learned from PCA of biomolecules, and here I want to mention what I find suspicious.

Fellowship of the RNA Society

published 2017-03-22

In May, I'll be traveling to Prague to a big conference about RNA. Good news has arrived: the registration fee will be reimbursed thanks to a travel fellowship I've received from the RNA Society. This is the first academic society I'm member of and it's just started paiyng off. I'm looking forward to visiting the city, where I spent ten wonderful years.

RNA Society

Web of Science Hot Paper

published 2017-03-11

Great news! In December 2016, our review on sigma-hole calculations was ranked by Thomson Reuters Web of Science in the top 0.1 % of the academic field of chemistry.

Hot paper