FoldX plugin for YASARA

Welcome to the homepage of the FoldX plugin for YASARA

FoldX tools menu in YASARA

The FoldX plugin for YASARA is a software package to access and run FoldX commands in YASARA.

FoldX is a molecular modeling and protein design software program that calculates energy differences that come close to experimental values. FoldX can minimize a PDB structure, mutate one or more residues to new residues, do protein stability analysis, protein-protein interaction energy analysis and much more. FoldX is widely used to predict the effect of mutations on the stability of a protein or to predict the effect on protein-protein binding.

YASARA is a molecular-graphics, -modeling and -simulation program that finally makes it really easy to answer your biological questions. The 3D graphics and intuitive interface make it a very user-friendly protein and nucleic acid analysis package. It is also easily extendable by means of plugins.

FoldX is normally run from the command line without graphics. By installing the FoldX plugin for YASARA, you can access the most important FoldX tools at the touch of a button in the 3D graphical YASARA interface. You directly see the results of your FoldX protein analysis on screen.

FoldX, YASARA and the FoldX plugin for YASARA are all available for Linux, MacOSX and Windows.

This website is a guide through the installation and usage of the FoldX plugin for YASARA.

Have fun!

Topics in this guide

• Installation and first use
• Guide of FoldX tools in YASARA
• Tutorial with real-world examples
• Troubleshooting
• Changelog

Miscellaneous

• Download PDF manual
• Request a new feature
• Citing the plugin
• List of research papers using the plugin
• Contact and support
• Special thanks
• More YASARA plugins from our group

Download

• FoldX plugin for YASARA version 4.1.21 (needs YASARA version 12.2.20 or higher)

Issues

• FoldX 3beta6 seems to be broken on MacOSX (certainly on 10.9.x systems), at least the BuildModel function (mutant analysis). I notified the developers and they are looking to fix this ASAP. My apologies.
• Ala scanning is broken for the moment because of new FoldX output files. I will fix this soon.

FoldX version information

Note: the new FoldX 3b6 released in january 2014 raised a segmentation fault on 64 bit systems and was therefore unusable on those machines. I tested the new version and it is now fixed.

FoldX 3 Beta 6 is required for the plugin to work. Any FoldX release before January 2014 will not work. Get the current version from http://foldx.crg.es.

YASARA version information

The plugin only works properly from YASARA version 12.2.20 and higher. Upgrading to the latest YASARA is strongly recommended.

Links

• foldx.crg.es FoldX website
• www.yasara.org YASARA website
• www.switchlab.org Switch Laboratory
• www.python.org Python website