Laboratory of Structural Biology and Cell Signaling

2020/10/19:
Pleasant colaboration with Haitin Lab on cis-prenyltrasferase made it from BioRXiv to Nature Communications!. Thanks EU_FT-ICR_MS H2020 Project for support!
2020/10/12:
Petr contributed to another community-wide paper stuffed with ideas and recommendations toward transparency and accessibility of data from cross-linking mass spectrometry. Check the full text!
2020/09/24:
Congatulations to Franta, now officially PhD in biochemistry!
2020/09/17:
Collaborative work with the team of Vaclav Veverka is now available in Structure.
2020/09/09:
Karel Vališ joined the Reviewer Board of Metabolites.
2020/09/07:
3D printing of MALDI targets is now published in Analytical Chemistry.

2020/09/04:
Call for EPIC-XS proposals is open till September 30, 2020. Next round will be till Dec 31, 2020! Submit via the online submission system.
2020/07/15:
Visitors coming to our lab from abroad should consult the web page of the Czech Ministry of Health regarding COVID-19 related travel restrictions.
2020/06/02:
We are looking for post-doc and PhD to join our team and work on various projects using structural mass spectrometry! Inquiries should be addressed to Petr Novak.
2019/03/27:
We are part of another Horizon 2020 project EPIC-XS (reg. no 823839) focused on the cutting edge proteomic techniques. This project provides Trans-National Access and also focuses on the development of the techniques.
2018/01/03:
Our lab is a part of Horizon 2020 project EU FT-ICR MS (reg. no 731077). Through this project you can access our expertise as well as other participating FT-ICR labs. Check Trans-National Acess web section for more details. Also, various FT-ICR focused courses and schools are organized by the labs participating in the project.
2017/12/20:
Bachelor and master theses are available in the lab. Areas of structrual biology, cutting edge mass spectrometry and cell signalling are awaiting new students. Check the tab Teaching.

Downloads

Software for interpretation of high-resolution MS data obtained after protein chemical cross-linking

The software is free to use, however the download is password protected. For access please contact Zdenek Kukacka. If you are using LinX for your research please consider to cite our work.

Download here

DeutEx - Software for interpretation of HDX-MS data will be available here.

The software is free to use, however is distributed upon signing of Software Transfer Agreement. The download is password protected. For access please contact Petr Man. If you are using these tools for your research please consider to cite our work.

Other HDX-MS related tools for data processing and visualization are below.

Digestion_metrics - Microsoft Excel macro calculating simple digestion metrics (coverage, average peptide length, redundancy, etc.) Modified supplementary file to publication Kadek A et al Anal Chem. 2014, 86(9):4287-94.
HDXPeptideSplitter - Python script for preporcesing of HDX-MS results before using them in PyMol. Processed data are then used by data2bfactor Pymol script written by Robert L. Campbell. This version works with Python version 2.x. For version 3.x and higher use this modified data2bfactor script.

An integrated computational platform for biomolecular language processing

MatrixMotif, our novel hybrid algorithm for biomolecular language processing has been successfully applied during mining of hidden TFBS motifs from enriched NGS datasets. We primarily stacked on Hypergeometric Distribution Model allowing pseudo-random estimation of DNA motif seeds which are subsequently marginalized through eigenvalue of the Markov chain transition matrix. To get rid of local optima in our constraints we were iterating our motifs using property of Maximum Entropy to maximize our expectation. The maximum free motifs are then re-estimated using hidden Markov matrix and the SuperBinder motif is selected according its maximum log-likelihood score. Now we are hoping in the Docker daemon to come with MatrixMotif container as soon as possible. MatrixMotif chomps all models through SciPy and CRAN ecosystems under UNIX-like systems.
Individual R packages can be downloaded via the CRAN network (mHG, mHMMbayes, DCAM, IMMIGRATE, modeLLtest).

The software is free to use, final integrated package is under construction. In you need any assistance or more information please contact Karel Valis.