Tehdyt toimenpiteet
Rosetta at CSC
Version
Rosetta version 3.1 is available in Hippu.csc.fi
Description
ROSETTA is a software suite for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions. The Rosetta suite provides following functions
- RosettaAbinitio Performs de novo protein structure prediction.
- RosettaDesign Dentifies low free energy sequences for target protein backbones.
- RosettaDock Predicts the structure of a protein-protein complex from the individual structures of the monomer components.
- RosettaAntibody Predicts antibody Fv region structures and performs antibody-antigen docking.
- RosettaFragments Generates fragment libraries for use by Rosetta ab initio in building protein structures.
- RosettaNMR Incorporates NMR data into the basic Rosetta protocol to accelerate the process of NMR structure prediction
- RosettaDNA For the design of proteins that interact with specified DNA sequences.
- RosettaRNA Fragment assembly of RNA.
- RosettaLigand For small molecule - protein docking
Usage
Please register your self as Rosetta user in the Rosetta home page before starting to use Rosetta.
To set up Rosetta commands in Hippu, give command:
module load rosetta
After that you can use the Rosetta 3.0 commands. Please be sure to check the Rosetta commands form the latest Rosetta 3.0 manual, as the usage differs significantly from older Rosetta versions. For example predicting a De Novo structure for a given sequence could be done with following commands:
1. First create a set of fragment libraries for the sequence with command:
make_fragments.pl sequence.fasta -id TEST1 -nosam -nojufo -noprof
Executing this command takes few minutes and it produces the 3-mer fragment file( aaTEST103_05.200_v1_3) and 9-mer fragment file ( aaTEST109_05.200_v1_3). These files are needed for the actual De Novo prediction.
2. Run the De Novo prediction
The De Novo prediction is done with Rosetta command: AbinitioRelax.linuxgccrelease. A simple structure prediction could now be executed with command:
AbinitioRelax.linuxgccrelease -in:file:fasta sequence.fasta -in:file:frag9 aaTEST109_05.200_v1_3 \
-in:file:frag3 aaTEST103_05.200_v1_3 -out:pdb -out:file:silent OUT \
-out:nstruct 5 -abinitio -database $ROSETTADB
Examples of other Rosetta 3.1 commands can be found from the rosetta3_demos directory. In Hippu the location of this directory is:
/v/linux26_x86_64/appl/molbio/rosetta/3.1/rosetta_demos
More information
| Mattila Kimmo | Kimmo.Mattila at csc.fi |
