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

2021/05/10:
EPIC-XS organizes regular workshops/webinars. The third one, on Clinical proteomics, will be on June 17, 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.
2021/04/27:
Call for EPIC-XS proposals is open till June 30, 2021. Next round will be till Sep 30, 2021! Submit via the online submission system.
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.

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.