Difference between revisions of "Solubis plugin for YASARA"
(Created page with "__NOTOC__ <big>'''Welcome to the homepage of the FoldX plugin for YASARA'''</big> thumb|500px|FoldX tools menu in YASARA The FoldX plugin for YASARA i...") |
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__NOTOC__ | __NOTOC__ | ||
| − | <big>'''Welcome to the homepage of the | + | <big>'''Welcome to the homepage of the Solubis plugin for YASARA'''</big> [[File:Foldx_menu.png|thumb|500px|Solubis tools menu in YASARA]] |
| − | The | + | The Solubis plugin for YASARA is a software package to identify mutants that decrease the aggregation tendency with YASARA. This package combines TANGO, WALTZ, FoldX and YASARA. |
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| + | '''TANGO''' is a statistical mechanics algorithm that identifies the regions of a protein sequence involved in the process of b-sheet aggregation. | ||
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| + | '''WALTZ''' | ||
'''FoldX''' is a molecular modeling and protein design software program that calculates energy differences that come close to experimental values. | '''FoldX''' is a molecular modeling and protein design software program that calculates energy differences that come close to experimental values. | ||
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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 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. | + | TANGO, WALTZ, 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 | + | This website is a guide through the installation and usage of the Solubis plugin for YASARA. |
Have fun! | Have fun! | ||
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== Topics in this guide == | == Topics in this guide == | ||
* [[Installation and first use]] | * [[Installation and first use]] | ||
| − | * [[ | + | * [[Solubis tools in YASARA|Guide of Solubis tools in YASARA]] |
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* [[Troubleshooting]] | * [[Troubleshooting]] | ||
* [[Changelog]] | * [[Changelog]] | ||
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== Miscellaneous == | == Miscellaneous == | ||
* [[Media:FoldXYasaraPluginManual.pdf|Download PDF manual]] | * [[Media:FoldXYasaraPluginManual.pdf|Download PDF manual]] | ||
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* [[Citing|Citing the plugin]] | * [[Citing|Citing the plugin]] | ||
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* [[Contact|Contact and support]] | * [[Contact|Contact and support]] | ||
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== Download == | == Download == | ||
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== Links == | == Links == | ||
| + | * [http://tango.crg.es tango.crg.es] TANGO website | ||
| + | * [http://waltz.crg.es waltz.crg.es] WALTZ website | ||
* [http://foldx.crg.es foldx.crg.es] FoldX website | * [http://foldx.crg.es foldx.crg.es] FoldX website | ||
* [http://www.yasara.org www.yasara.org] YASARA website | * [http://www.yasara.org www.yasara.org] YASARA website | ||
* [http://www.switchlab.org www.switchlab.org] Switch Laboratory | * [http://www.switchlab.org www.switchlab.org] Switch Laboratory | ||
* [http://www.python.org www.python.org] Python website | * [http://www.python.org www.python.org] Python website | ||
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Revision as of 19:13, 15 March 2013
Welcome to the homepage of the Solubis plugin for YASARA
The Solubis plugin for YASARA is a software package to identify mutants that decrease the aggregation tendency with YASARA. This package combines TANGO, WALTZ, FoldX and YASARA.
TANGO is a statistical mechanics algorithm that identifies the regions of a protein sequence involved in the process of b-sheet aggregation.
WALTZ
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.
TANGO, WALTZ, 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 Solubis plugin for YASARA.
Have fun!
Topics in this guide
Miscellaneous
Download
- FoldX plugin for YASARA version 2.8.6 (needs YASARA version 12.2.20 or higher)
FoldX version information
FoldX 3 Beta 5.1 is required for the plugin to work. Any FoldX release before January 2013 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
- tango.crg.es TANGO website
- waltz.crg.es WALTZ website
- foldx.crg.es FoldX website
- www.yasara.org YASARA website
- www.switchlab.org Switch Laboratory
- www.python.org Python website
