About

The FoldX consortium

FoldX was developed by the FoldX consortium, centered around the laboratory of Luis Serrano at the European Molecular Biology Laboratory in Heidelberg and at Center for Genomic Regulation in Barcelona. The following people have contributed to the development to different extents:

• Raphael Guerois • Jens Nielsen • Jesper Borg • Peter Vanhee • Erik Verschueren • Lies Baeten • Javier Delgado • Joost Schymkowitz • Frederic Rousseau • Francois Stricher • Luis Serrano

 

Intellectual Property

Intellectual property issues up to version 2.6 are handled by EMBLEM. Executables are only available to be downloaded from our website, based on a material transfer agreement (MTA) with EMBLEM.

Version 3.0 and the FoldX Suite are handled by the CRG Technology and Business Development Office
Version 3.0 is still available at foldx.crg.es.

 

News

The FoldX Suite includes several improvements over former versions of FoldX:

New InterpretiX smart engine:

  • Based on C++/Boost Command Line Interface
  • Encapsulation of different software packages
  • Unified Command Line Interface and executable to launch different modeling tools
  • Better error reporting of any problems with the command line
  • Unified human-readable configuration file to work with different modeling tools (no more ‘XML-like’ syntax)
  • High level programming layer, to combine different FoldX commands in a flexible and iterative way to generate complex analysis
  • Interactive help on general and specific parameters
  • Integration of a new FoldX Driver for parallel usage on cluster supporting the Java Sungrid Engine

New modeling packages, exploiting the power of fragment libraries:

  • LoopX: allows fast and accurate prediction of protein loop structure by means of LoopXDB, a library of non-regular structure elements, clustered according to end-to-end distance between the regular residues flanking the loop PepX: allows fast and accurate prediction of peptide docking by means of BackXDB, a library of protein building blocks, and PepXDB, a library of protein-peptide binding motifs
  • BackX (long term future)
  • DnaX (long term future)
  • The BackXDB, LoopXDB and PepXDB databases were formerly known as Brix, LoopBrix and InteraX

New commands:

  • PSSM (Position Specific Scoring Matrices): it combines the ‘buildmodel’ and ‘analysecomplex’ commands. It mutates selected positions to a list of provided residues and after that it calculates the difference of interaction free energies (DDG) upon mutation.
  • Domino (not yet integrated): for iterative PSSM based refinement

Parametrization of new molecules:

  • 1,2-dioctadecyl-3-phosphatidyl-choline parameters allows modeling of lipid bilayers

AncoraAncora

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Office:

Centre for Genomic Regulation (CRG)
C/ Dr. Aiguader, 88
PRBB Building
08003 Barcelona, Spain