My First Publishing Contribution to the Field of Psychology
I studied a bit of Principle Component Analysis (PCA) and other data-analysis methods in the context of emotional analysis of a text. Surprisingly, it is closely related to my expertise in biomolecular simulations. My short report about the conjunction of text and biomolecular analysis has recenly been published in a Czech popular-science magazine Vesmír (pay-walled). Strangely enough, the editorial office classified the piece into a psychology section. It seems that the scope of my research expands:-)
Publications Available on the arXiv Preprint Server
From now, some of my publications are available on the preprint server arXiv. Please visit a dedicated page for a list of them, or check a full list of my articles. I'll keep on uploading my preprints there if possible. In other cases feel free to contact me and ask for a PDF.
Tutorial: How to Visualize a Molecular Electrostatic Potential with Molekel
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:
Helmut's Department of Theoretical and Computational Biophysics has a brand new group photo.
J. Med. Chem. Perspective
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.
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
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.
I've just received a rubber stamp.
Emotional Arcs and Random Diffusion
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.