Mechanochembio 2017 in Berlin
last update 2017-10-16
Here I put a few videos that are related to my talk and poster contribution at the Multiscale Mechanochemistry and Mechanobiology 2017 conference in Berlin. The conference takes place in the Harnack Haus, which I find, already after a couple of minutes of being here, an absolutely amazing place to meet.
Assistant Professor at UCT
My new employer will be the University of Chemistry and Technology in Prague. I got an assistent professor position at the Department of physical chemistry. My first duties are related to a course of Spectroscopic methods. Looking forward to starting full time in January 2018.
Ribosome Review Submitted
A review on computer simulations of the ribosome has just been submitted to Current Opinion in Structural Biology. The simulation work on cellular translation grows almost explosively. Our work with Lars and Helmut reviews a fraction of literature from about last 5 years. This is how the graphical abstract of the paper was prepare.
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