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Rosetta at CSC

Version

Rosetta version 3.2 is available in Hippu.csc.fi and in Vuori.csc.fi


Description

ROSETTA is a software suite for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions. The Rosetta suite can be used for example for following tasks:

  • Perform sequence based de novo protein structure prediction.
  • Predict the structure of a protein-protein complex from the individual structures of the monomer components.
  • Predict structures of protein-peptide complexes with flexible peptide models
  • For small molecule - protein docking
  • Predict antibody Fv region structures and perform antibody-antigen docking.
  •  For the design of proteins that interact with specified DNA sequences.
  • Comparative homology modeling
  • predict  the structure of homooligomeric protein assemblies starting from the structure of a single subunit.

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 or Vuori, give command:
module load rosetta

After that you can use the Rosetta commands.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 (note that make_fragments.pl command does not work in Vuori ) :
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 3.2 commands can be found from the rosetta3_demos directory. In Hippu the location of this directory is:

/v/linux26_x86_64/appl/molbio/rosetta/3.2/rosetta-3.2/rosetta_demos


 More information

Mattila Kimmo Kimmo.Mattila at csc.fi