Running Proteasome on Hazel Hen

published 2018-04-27

Hazel Hen, one of the largest supercomputers in Europe, has just "opened its processors" to our simulations. Our large-scale computational project has been awarded 40 million core-hours, which is a nice chunk of the supercomputing power. For comparison, it is equivalent to almost 70% of the power, which was provided for the whole Czech computational community by IT4I in its last call.

Human proteasome

So in the next 12 months, we will run all-atom molecular dynamics simulations of the human proteasome. It is a large biomolecular complex responsible for protein degradation. Interestingly, a few drugs and drug candidates act through affecting proteasome function. We will try to uncover, how these drug affect proteasome choreography.

Current Opinion Cover Page

published 2018-04-26

The Current Opinion in Structural Biology has featured our contribution on the journal cover page. Upon invitation, Helmut, Lars and me submitted a review to a special issue on Theory and simulation. Although the paper has been available since last year, the issue was released just last week. I have already posted a video about how the cover picture was done.

Current Opinion Cover Page

Making of Group Poster

published 2018-04-11

I've prepared a poster about our research group. This is how it has evolved.

The unstalled tnaC nascent peptide in the ribosome

Another nascent peptide in the ribosome tunnel. This is a so called tnaC peptide through which the ribosome senses a level of free tryptophane. The figure shows several tnaC conformations as obtained in several μs-long molecular dynamics simulations in the absence of free tryptophane.

published 2018-03-09

IT4I Project Approved

published 2018-01-30

The Czech supercomputing center IT4I in Ostrava is the largest facility of this kind in the Czech Republic. To date, its supercomputer Salomon is ranked around 90th place worldwide. I applied to the latest call with a simulation project which deals with a ribosome-regulatory peptide VemP. VemP regulates translation of two bacterial gene variants by modulating the catalytic center of the ribosome. The project received an allocation of about 420 thousand corehours. Compared to our previous LRZ computational project, it is a tiny amount, but I hope it will anyway help us clarify the role of environment on the VemP structure and dynamics. The figure show the VemP in the ribosome exit tunnel. We will simulate the VemP in neat water.

VemP peptide in the ribosome exit tunnel'

Publication Overview 2017

published 2018-01-19

The whole world of research seems to be obsessed by scientometry. Unfortunately, questions like "how many papers" or "what is the impact factor" replace questions, which may bring truly new advances and insights. The discussion with my colleagues are full of "papers" and "citations". Having a fresh experience from Germany, I feel the contrast even stronger here in Czechia. No wonder, the reason is clear: in the Czech Republic, the science funding depends strongly on the scientometric criteria of the applicant. Certain adaptation to this external pressure is inevitable for any scientist who really means it, now matter one agrees or disagrees with it. Here is my piece of the obsession. During 2017, I monitored my Google Scholar account using a simple python script. I provide a few observations, which attracted my attention.

Moving to Prague

published 2018-01-02

In January 2018, my primary work address changed. I moved (back) to Prague - the heart of Europe. I'm starting an assistant professor position at the University of Chemistry and Technology (UTC). It's only 20 min walk from the Prague castle, 15 min ride from the Vaclav Havel Airport. I keep on studying biomolecular complexes using (super)computers and will be happy to accept informal inquiries from enthusiastic students or postdocs. Just write me an email...

All the best in 2018

There seems to be a Christmas tree inside the ribosome. All the best in 2018.

published 2018-01-02

Conference at Downing College

published 2017-12-11

Yesterday I arrived to Cambdrige to join a meeting on co-translational folding and nascent peptides. There would be hardly a better-matching topic to what I'm working on in Göttingen. After the first day of talks, I'm looking forward to the remaining two.

Downing College in Cambridge after a snow 'storm'

Our Review on Ribosome Simulations Available on arXiv

published 2017-11-16

Well, the main message is in the heading. The preprint of our review is here: The paper has just been accepted in Current Opinion in Structural Biology and should be published in April 2018 issue.

A structure of the bacterial ribosome with a scheme of bacterial translation