flexible-meccano

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 :

 version MAC :

CNIL

No personal data is collected, passed to third parties or used without your knowledge. In accordance with the French Data Protection Act 78-17 of 6 January 1978 and amendments thereto, you have the right to access, modify or remove your personal data. You can exercise this right by writing to Institut de Biologie Structurale J.P. Ebel, 41, rue Jules Horowitz F-38027 GRENOBLE Cedex 1. The user can consult information concerning their rights, duties and the protection of personal data on the Commission Nationale Informatique et Libertés (French data protection authority) website (http://www.cnil.fr)
This page has been registered with the CNIL: ref. No. 1572130