Laboratory of Structural Biology and Cell Signaling

2019/08/05:
5th Short Course on FT-ICR-MS aimed at "Basics of FT-ICR: dynamic harmonization and computer simulation" will be held in early October in Moscow. Apply now, no participation fee, accommodation and meals covered!
2019/07/24:
Preprint version of our paper combining structural MS approaches for characterization of transcription factor / DNA interaction is now available in Biomolecules.
2019/07/19:
Chromatin Proteomics Workshop coorganized by EPIC-XS H2020 consortium will be on Sep 22-27, 2019 in Greece. Deadline (Jul 29) is approaching!.
2019/07/15:
Two new papers dealing with HDX-MS are out. In one we contributed to very important community wide guidelines paper in Nat. Methods - Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. Antoher one is a joint Anal. Chem. paper with Kasper Rand's lab on HDX-compatible digestion of membrane proteins.
2019/07/10:
Joint paper with Valasek's lab describing how chemical cross-linking helps in structural characterization of 40S ribosomal subunit interacting with eIFs is now available in Nucleic Acid Research.
2019/07/10:
Short course on High Resolution Tandem Mass Spectrometry of Biomolecules will be organized by the EU_FT-ICR_MS H2020 consortium. Save the date and place: Aug 21-23, 2019, Warwick. Register here.

2019/08/15:
Do you want to analyze your samples at some top European proteomics lab? Apply for the access within the EPIC-XS consortium. Second round of submissions closes on Sep 30, 2019.
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.

Here you can find various 3D printed things, mostly generated by Dan Kavan. Fell free to use them! We will always provide FreeCAD files together with *.stl and some basic comments.

Our passion in 3D printing is strongly supported by a collaboration with the TRILAB company.