Downloads
LinX
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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.
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.
HDX tools
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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.
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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.
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Soubory cvičení "Úvod do proteomické analýzy s využitím hmotnostní spektrometrie" na 21. Škole hmotnostní spektrometrie, Srní 13.-18.9.2020.
MALDI peptide mass mapping files
MatrixMotif
An integrated computational platform for biomolecular language processing
Škola MS, Srní 13.-18.9.2020
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