Rosetta High Resolution Protein Structure Refinement Protocol: Difference between revisions

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== '''Rosetta High Resolution Protein Structure Refinement Protocol''' ==
== '''Introduction''' ==


[http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/rosetta.php Rosetta] is a molecular modeling software package developed in the Baker Laboratory (U. of Washington) for the study and prediction of protein structures, and protein-DNA and protein-protein interactions.


Before running Rosetta, please make directory with:
== ''''''Protocol'''''' ==
* rosetta_database (directory)
**  paths.txt
**  1pdb.pdb (PDB file for single xray or nmr structure, with chain A reference removed)
**  1pdb_.fasta (containing full length sequence)
**  aa1pdb_03_05.200_v1_3  (3mer fragment files generated for 1pdb sequence)
**  aa1pdb_09_05.200_v1_3  (9mer fragment files generated for 1pdb sequence)
Note:  fragment files can be obtained from the [http://robetta.bakerlab.org/fragmentsubmit.jsp  Robetta fragment server].


Before running Rosetta, please make directory with:


=== '''X-ray Structure Refinement''' ===
*rosetta_database (directory)
#  Input pdb files into Rosetta format
**paths.txt
#  Add "missing" residues, such as N- and C-term, relax
**1pdb.pdb (PDB file for single xray or nmr structure, with chain A reference removed)
#  Idealize geometry
**1pdb_.fasta (containing full length sequence)
#  Relax single input structure with backbone perturbations and sidechain repacking.
**aa1pdb_03_05.200_v1_3 (3mer fragment files generated for 1pdb sequence)
**aa1pdb_09_05.200_v1_3 (9mer fragment files generated for 1pdb sequence)


=== '''NMR Structure Refinement''' ===
Note: fragment files can be obtained from the [http://robetta.bakerlab.org/fragmentsubmit.jsp Robetta fragment server].
 
<br>
 
=== '''X-ray Structure Refinement'''  ===
 
#Input pdb files into Rosetta format
#Add "missing" residues, such as N- and C-term, relax
#Idealize geometry
#Relax single input structure with backbone perturbations and sidechain repacking.
 
=== '''NMR Structure Refinement''' ===
 
#Input pdb files into Rosetta format
#Add "missing" residues, such as N- and C-term, relax (not needed If NMR structure is for full length sequence)
#Idealize geometry
#Rebuild loops, relax and minimize
 
=== '''Commands'''  ===


#  Input pdb files into Rosetta format
# Add "missing" residues, such as N- and C-term, relax (not needed If NMR structure is for full length sequence)
#  Idealize geometry
#  Rebuild loops, relax and minimize
=== '''Commands''' ===
  <nowiki>
  <nowiki>
# rosetta -score -fa_input -s xxxx.pdb -nstruct n -use_pdb_numbering
# rosetta -score -fa_input -s xxxx.pdb -nstruct n -use_pdb_numbering
Line 34: Line 42:
</nowiki>
</nowiki>


=== '''Files for Download''' ===
=== '''Files for Download''' ===
* Click to download [[NESG:%ATTACHURL%/Rosetta_Protocol.doc|Rosetta_Protocol.doc]]: Rosetta protocol in word format
 
* Click to download [[NESG:%ATTACHURL%/example_NMR_rosetta_refinement.tar.gz|example_NMR_rosetta_refinement.tar.gz]]: Example files for NMR Rosetta Refinement
*Click to download [[NESG:%ATTACHURL%/Rosetta Protocol.doc|Rosetta_Protocol.doc]]: Rosetta protocol in word format  
* Click to download [[NESG:%ATTACHURL%/example_Xray_rosetta_refinement.tar.gz|example_Xray_rosetta_refinement.tar.gz]]: Example files for Xray Rosetta Refinement
*Click to download [[NESG:%ATTACHURL%/example NMR rosetta refinement.tar.gz|example_NMR_rosetta_refinement.tar.gz]]: Example files for NMR Rosetta Refinement  
*Click to download [[NESG:%ATTACHURL%/example Xray rosetta refinement.tar.gz|example_Xray_rosetta_refinement.tar.gz]]: Example files for Xray Rosetta Refinement

Revision as of 23:05, 5 November 2009

Introduction

Rosetta is a molecular modeling software package developed in the Baker Laboratory (U. of Washington) for the study and prediction of protein structures, and protein-DNA and protein-protein interactions.

'Protocol'

Before running Rosetta, please make directory with:

  • rosetta_database (directory)
    • paths.txt
    • 1pdb.pdb (PDB file for single xray or nmr structure, with chain A reference removed)
    • 1pdb_.fasta (containing full length sequence)
    • aa1pdb_03_05.200_v1_3 (3mer fragment files generated for 1pdb sequence)
    • aa1pdb_09_05.200_v1_3 (9mer fragment files generated for 1pdb sequence)

Note: fragment files can be obtained from the Robetta fragment server.


X-ray Structure Refinement

  1. Input pdb files into Rosetta format
  2. Add "missing" residues, such as N- and C-term, relax
  3. Idealize geometry
  4. Relax single input structure with backbone perturbations and sidechain repacking.

NMR Structure Refinement

  1. Input pdb files into Rosetta format
  2. Add "missing" residues, such as N- and C-term, relax (not needed If NMR structure is for full length sequence)
  3. Idealize geometry
  4. Rebuild loops, relax and minimize

Commands

# rosetta -score -fa_input -s xxxx.pdb -nstruct n -use_pdb_numbering
# rosetta aa 1pdb _ -relax -looprlx -s <your input file > -fa_input -loop_file  <loop_file_name> -nstruct1    
# rosetta -pose_idealize -s <input file name> -fa_input -nstruct 1
# rosetta aa 1pdb _ -relax -farlx -looprlx -loop_file <loop_file_name> -ex1  -ex2 -fa_input -s <input pdb file> -random_loop -loop_skip_rate 0.3 -farlx_cycle_ratio 1.0 -full_filename -nstruct < number of structures you want>
# rosetta aa 1pdb _ -relax -farlx -s <input pdb file> -fa_input -ex1 -ex2 -short_range_hb_weight 0.50 -long_range_hb_weight 1.0 -farlx_cycle_ratio 1.0 -full_filename -nstruct <as many structures as you want>

Files for Download

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