Laboratory of Structural Biology and Cell Signaling

2020/01/08:
Our new computational platform for biomolecular language processing called MatrixMotif is now available for download.
2020/01/07:
Petr Novak became the chair of the Czech Proteomics Society. Congratulations! :)
2020/01/07:
6th Short Course on FT-ICR-MS aimed at "Mapping post-translational modifications through FT-ICR" will be held in Lisbon in March 2020. Apply now, no participation fee, accommodation and meals covered!
2019/12/18:
Long-lasting, nice and enjoyable collaboration with Gill Norris from Massey University (NZ) resulted in one more paper on bacterions. Now published in FEBS Letters.
2019/12/12:
Results of another TNA access under EU_FT-ICR_MS H2020 Project are now in the FEBS Journal. Collaboration with the University of Pavia, Italy.
2019/12/11:
TNA access under EU_FT-ICR_MS H2020 Project gave rise to this nice paper on NQO1 dynamics. Collaboration with Angel L. Pey from the University of Granada, Spain.

2020/01/07:
Call for EPIC-XS proposals was closed on Dec 31, 2019. Get ready for next round which closes on March 31, 2020! Submit via the online submission system.
2019/11/12:
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

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, IMIGRATE, 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.

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.