View source for FoldX plugin for YASARA

__NOTOC__
<big>'''Welcome to the homepage of the FoldX plugin for YASARA'''</big> [[File:Foldx_menu.png|thumb|500px|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!

== News ==
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'''We are very pleased to announce that the FoldX plugin for YASARA has been published in [http://dx.doi.org/10.1093/bioinformatics/btr254 Bioinformatics]!'''<br>
Citation details are right over [[Citing|here]].
</div>

== Topics in this guide ==
* [[Installation and first use]]
* [[FoldX tools in YASARA|Guide of FoldX tools in YASARA]]
* [[Training exercises|Tutorial with real-world examples]]
* [[Troubleshooting]]
* [[Changelog]]

== Miscellaneous ==
* [[Media:FoldXYasaraPluginManual.pdf|Download PDF manual]]
* [[Request a new feature]]
* [[Citing]]
* [[Contact|Contact and support]]
* [[Special thanks]]
* [[More YASARA plugins from our group]]

== Download ==
* [[Media:Foldxyasara.zip|FoldX plugin for YASARA version 1.4.22]]

== FoldX version information ==

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'''FoldX 3 Beta 5 is required for the plugin to work. The Beta 4 has expired and doesn't work anymore. Get the new version from [http://foldx.crg.es http://foldx.crg.es].'''
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== YASARA version information ==

<div style="background:#FADADD;border:1px solid #FFC0CB;">
'''The plugin only works properly from YASARA version 10.11.22 and higher. Upgrading to the latest [http://yasara.org/downloads.htm YASARA] is strongly recommended.'''
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== Links ==
* [http://foldx.crg.es foldx.crg.es] FoldX website
* [http://www.yasara.org www.yasara.org] YASARA website
* [http://switch.vub.ac.be switch.vub.ac.be] Switch Laboratory
* [http://www.python.org www.python.org] Python website

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