Laboratory of Structural Biology and Cell Signaling

2021/06/15:
We are organizing 2nd Advanced User School under the H2020 EU_FT-ICR_MS consortium. The school will be held in Prague/Vestec, Czech Republic on September 26-30, 2021 and will be stuffed with basics and applications of FT-ICR MS. Participation fee, accommodation and meals covered for 50 selected participants. Registration form can be found HERE. Deadline for application - Aug 23, 2021. Entry to CZ is regulated according to actual COVID situation.
2021/05/31:
Petr's collaboration with the Volf's lab and Austrian's parasitologists is now published in Parasit. Vectors.
2021/04/21:
Proteomic analysis of F. pinicola secretome leading to expression and characterization of two laccases (collaboration with the Ludwig Lab) has just been accepted in Enzyme Microb Technol
2021/04/09:
Structural analysis of human haptoglobin by FPOP and the benefits of ion mobility (TIMS/PASEF) for such analysis is now published in ACS Omega
2021/03/25:
Structural aspects of Von Willebrand factor binding and processing by metallopeptidase ADAMTS-13 studiedby integrative structural biology. Trans-national access via the EPIC-XS resulted in a joint publication in J. Mol. Biol.
2021/03/10:
The results of collaboration with the parasitology groups from Charles University and Morroco are now published in Transboundary and Emerging Diseases

2021/07/20:
Call for EPIC-XS proposals is open till Sep 30, 2021. However the pipeline is already quite full, so limited number of proposals can be accepted. Submit via the online submission system.
2021/07/20:
EPIC-XS organizes regular workshops/webinars. The fourht one, on Spatial proteomics, will be on Aug 26, 2021. Check EPIC-XS web site for details.
2021/04/27:
We are looking for post-doc with knowledge of excimer lasers and/or mass spec. Details here.
2020/04/01:
Are you interested in structural mass spectrometry, method development, transcription factors or membrane proteins? We are looking for Bc, MSc, PhD students and post-doc! Inquiries should be addressed to Petr Novak.

Downloads

Software for interpretation of high-resolution MS data obtained after protein chemical cross-linking. The software is free to use. If you are using LinX for your research please cite the related publication.

Download here

This software is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 731077P.

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 pre-processing of HDX-MS results before using them in PyMol. Processed data are then loaded through 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.