Laboratory of Structural Biology and Cell Signaling

2019/01/26:
Joint paper with Ales Hnizda on structural characterization of pyrophosphatase NUDT15 and its thiopurine intolerance causing mutations is now available in Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics.
2018/11/28:
We recieved funding from Czech Science Foundation to study protein structure by reactive radical footprinting and top-down mass spectrometry.
2018/11/20:
Paper on Hsp70 dimerization - our collaboration with RECAMO team - has just been accepted in Mol Cell Proteomics.
2018/11/08:
Our work about structure of NK cell receptor Nkrp1b is now in Journal of Proteomics.
2018/09/13:
We are proud to be a part of another EU Horizon 2020 project called EPIC-XS (European Proteomics Infrastructure Consortium providing Access).

2018/10/11:
2nd International HDX MS Conference will be May 21-24, 2019 in Banff, Canada.
2018/07/13:
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.
2018/06/25:
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.