On this page you can find descriptions and links to download free software that is often used to assist in research analysis, chromatography as well as peptide and protein modelling / design.
We do not program any software ourselves and cannot offer support for these applications, however we have found them to be useful in the lab.
Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.
OpenChrom is an open source software for chromatography, spectrometry and spectroscopy. Data from different systems can be imported and analyzed, hence it’s a vendor independent software. Moreover, it runs under Windows, macOS and Linux. So the user has the choice to work wherever he wants, independent of the system. Originally, the intention was to create a ChemStation alternative. Meanwhile, it has become much more. Generally, it supports to handle GC/MS, GC/FID, HPLC-UV/VIS, FTIR, PCR and NMR data.
PeakSimple software has been continuously developed, refined, and improved since 1988 by a dedicated team of working chromatographers. These chromatographers use the software on a daily basis, and strive to simplify and enhance every aspect of PeakSimple so our customers will benefit. New features are added to PeakSimple several times per year, and the lates version is always FREE to download online, along with helpful tutorials.
MZmine 2 is an open-source software for mass-spectrometry data processing, with the main focus on LC-MS data. It is based on the original MZmine toolbox described in the 2006 Bioinformatics publication, but has been completely redesigned and rewritten since then. Our main goal is to provide a user-friendly, flexible and easily extendable software with a complete set of modules covering the entire LC-MS data analysis workflow.
UniChrom is fully automated Chromatographic Data System, dedicated to simplify hard, routine work of Chemist, dealing in a field of Gas and Liquid Chromatography.
The PEPstrMOD server predicts the tertiary structure of small peptides with sequence length varying between 7 to 25 residues. It also handles peptides having various modifications like non-natural residues, terminal modifications (Acetylation/Amidation), Cyclization (N-C, disulfide bridges), conversion of L- to D- amino acids, post translational modifications, etc. The prediction strategy is based on the realization that β-turn is an important and consistent feature of small peptides in addition to regular structures. Thus, the method uses both the regular secondary structure information predicted from PSIPRED and β-turns information predicted from BetaTurns. The structure is further refined with energy minimization and molecular dynamic simulations.
PeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data!
