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Institut de Biologie StructuraleGrenoble / France

Contact person(s) related to this article / OZENNE valery

flexible-meccano

Pour la version française du site, cliquer sur le lien ci-dessous:

http://www.ibs.fr/science/production-scientifique/logiciels/flexible-meccano-678/?lang=fr

Update

Recent updates are now available. A web protocol is now in charge of an automatic update on your computer. For bug reporting or program support, please provide a brief description of the problem at flexible-meccano@ibs.fr

9th of january 2013 / Mac version

  • A Mac version (beta version) of flexible-meccano has been released
  • A 5’ movie shows new functionalities : click HERE

16th of october 2012 / Linux version

  • A new version of flexible-meccano has been released
  • A 3’ movie shows new functionalities : click HERE

4th of june 2012 / Linux version && Mac version

  • New manual : how to use flexible-meccano via the command line ?

29th of may 2012 / Linux version

  • Contact calculation was not taken into account for sequences beginning by a number different from one ..... revised
  • PDB writing : space between columns was missing for proteins containing more than 1000 atoms ..... revised
  • PDB writing : special correction for proteins ending with a glycine ..... revised

Presentation of flexible-meccano

The program was originally developed to generate ensembles of realistic atomic models that are compatible with biophysical data measured using NMR and SAXS. flexible-meccano randomly samples amino-acid-specific backbone dihedral angle φ/ψ propensities derived from non-secondary structural elements of high-resolution X-ray crystallographic structures,and thereby assembles a conformational ensemble from which experimental values can be calculated. Amino-acid specific hard-sphere steric clashes are used to provide a physically reasonable model of repulsive interatomic forces, and no attractive forces are explicitly used. The simplicity of the model allows for highly efficient structure ensemble assembly (100,000 structures of a 100 amino acid protein can be created in 30 minutes on a single processor). It has now been entirely rewritten, updated and interfaced to include the following NMR calculations:

  • Residual dipolar couplings
  • Paramagnetic Relaxation Enhancement
  • J coupling

Documentation, Movies

Two short movies presenting the main functionalities are available :

  • Click HERE (Launch a simulation from scratch )
  • Click HERE (Presentation of the graphical functionalities)

The program is delivered with example protocols and data and is fully documented. It has been compiled for the following platforms :

  • PC Linux running Redhat
  • Mac (beta version)

Contact : flexible-meccano at ibs.fr

The license is free for academic sites and non commercial use.


References

If any results obtained with the flexible-meccano program are published, whatever the means of publication, particularly in the scientific literature, the program should be referenced in the following way:

Flexible-meccano: a tool for the generation of explicit ensemble descriptions of intrinsically disordered proteins and their associated experimental observables, Valery Ozenne; Frederic Bauer; Loic Salmon; Jie-rong Huang; Malene Ringkjobing Jensen; Stephane Segard; Pau Bernado; Celine Charavay; Martin Blackledge, Bioinformatics 2012 28: 1463-1470

Download

Before downloading the software, you must read the license.
If you agree the license terms, you can download the software :

- version PC :

Download
Software name : flexible-meccano
Your email (requested) :
Licence (requested) :
I accept the conditions of use
Your comments :
Note :
  • Email address is requested
  • A download link will be sent to this address (24h00 valid)
  • Your address will not be disclosed to anyone

- version MAC :

Download
Software name : flexible-meccano
Your email (requested) :
Licence (requested) :
I accept the conditions of use
Your comments :
Note :
  • Email address is requested
  • A download link will be sent to this address (24h00 valid)
  • Your address will not be disclosed to anyone

CNIL

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