CS-Rosetta

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Description

CS-ROSETTA is a framework for structure calculation of biological macromolecules on the basis of conformational information from NMR, which is built on top of the biomolecular modeling and design software called ROSETTA.

To date, interpretation of isotropic chemical shifts in structural terms is largely based on empirical correlations gained from the mining of protein chemical shifts deposited in the BMRB, in conjunction with the known corresponding 3D structures. Chemical-Shift-ROSETTA (CS-ROSETTA) is a robust protocol to exploit this relation for de novo protein structure generation, using as input parameters the 13CA, 13CB, 13C', 15N, 1HA and 1HN NMR chemical shifts. These shifts are generally available at the early stage of the traditional NMR structure determination procedure, prior to the collection and analysis of structural restraints. CS-ROSETTA utilizes chemical shift based selection of protein fragments from the PDB, in conjunction with Rosetta structure calculation.

License

You need to have a #licence to use CS-Rosetta. See Rosetta licence for instructions.

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of csrosetta and load default version of csrosetta as

module avail csrosetta/ # list available modules
module load csrosetta   # load (default) module


If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail csrosetta

and choose explicit version you want to use.

Documentation

Documentation is available on http://www.csrosetta.org/manual (http://spin.niddk.nih.gov/bax/software/CSROSETTA/index.html) of producer or locally in directory /software/rosetta/3.8/.

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