Software
Here we offer selection of our fully developed open-source software packages. For a list of minor software packages/tools associated to publication by our group, please see here.
MMMx
Toolbox for integrative protein ensemble modeling based on distance distribution information for determining ensemble width. Fully scriptable and extended successor of MMM for creating modeling pipelines. Visualization scripts require MMM, which must run in the same Matlab window.
Version 2023.2 corresponds to commit cc0b809 (April 3rd 2023) external pageon GitHub. external pageDocumentation and example set will be continuously extended.
external pageDocumentation (external web page)
DownloadMatlab source including resources (ZIP, 913.5 MB)
Unpack the ZIP file and add directory to the Matlab path.
DownloadWindows executable installer (EXE, 115.9 MB) (still version 1.1, inform us if you need this at a higher version)
Double-click the installer and follow instructions. Add directory to the Windows path. Open a windows command prompt and type MMMx docs to see the documentation.
DownloadExample set (ZIP, 4 KB)
Unpack the ZIP file. Double-click the MMMx icon and load one of the example .mcx files from the file browser window that opens. In Matlab, type 'MMMx' at the command prompt. You can also type MMMx with the .mcx file name as an argument at the command prompt. Typing 'MMMx docs' at the Matlab command prompt opens the documentation pages in a browser.
ComparativeDeerAnalyzer 2.0
Automatically analyzes DEER/PELDOR data sets in terms of distance distributions using neuronal network analysis and Tikhonov regularization. A consensus distribution and uncertainty estimate are computed. Quality parameters of the data are reported. Version 2.0 as of 2022/02/08 is more robust than version 1.0.
- DownloadStandalone installer for Microsoft Windows (EXE, 888.3 MB) (Matlab not required, runtime library downloaded during installation)
- DownloadShort manual (PDF, 690 KB) of CDA 2.0.
DeerLab
A comprehensive open-source Python package for the analysis of dipolar EPR spectroscopy data. Details on the homepage.
DeerAnalysis 2022
A program for extracting distance distributions from dead-time free pulsed electron electron double resonance (DEER, PELDOR) data with MATLAB, including DEERNet Rev. 5662 neural network processing. Version 2022 features neural networks for spin-1/2 RIDME (other background model) developed by Jake Keeley and Ilya Kuprov. It can process data with poorly fitting background better than earlier versions and issues a warning if mean distance is unreliable. Automatic comparative DEER analysis has become more robust. Version as of 2022/02/09.
DownloadDownload DeerAnalysis2022 (ZIP, 1001.8 MB)
MMM
An open-source program for visualization, inspection, generation, and improvement of models of proteins and protein assemblies based on restraints from multiple experimental techniques. Version 2024.1 implements a new spin label and two Alexa Fluor chromophores external pageSource code (GitHub)
DownloadDownload MMM 2024.1 (ZIP, 399.3 MB)
Hyscorean
An open-source package of EleXsys and Matlab software with graphical user-interface for acquiring non-uniform sampled HYSCORE data and for analyzing, both, uniform and non-uniform HYSCORE data, including validation and EasySpin-based fitting.