The scripts and input files that accompany this demo can be found in the demos/protocol_captures directory of the Rosetta weekly releases.

This is a protocol capture, and represents the protocol at a fixed point in time. It may not work with the current version of Rosetta.

KEYWORDS: PEPTIDES STRUCTURE_PREDICTION

Written by: Barak Raveh, Nir London, Lior Zimmerman, Ora Schueler-Furman

This is a protocol for the de-novo folding and docking of peptides to proteins (a major extension of the previous FlexPepDock refinement protocol) For this protocol, no initial information of the peptide backbone is requiered, only a placement of an arbitrary peptide strating structure of the peptide within the approximate binding pocket.

Setting up the demo

Before running the demo, make sure to change the following variables to you local environment:

FlexPepDockAbInitio/prepack_example:                 set PATH_TO_EXE and PATH_TO_DB
FlexPepDockAbInitio/run_example:                     set PATH_TO_EXE and PATH_TO_DB
FlexPepDockAbInitio/scripts/frags/make.sh:set        set PATH_TO_EXE and PATH_TO_DB
FlexPepDockAbInitio/scripts/clustering/cluster.sh:   set PATH_TO_EXE and PATH_TO_DB 
FlexPepDockAbInitio/scripts/prep_abinitio.sh:        set pathToDemo and pathToVall
FlexPepDockAbInitio/scripts/frags/make_fragments.pl: set $scratch and $pathToDemo

Running the demo

These flags are all found in input_files/flags:

IO flags:

-s start.ppk.pdb                                        # The start structure of the peptide-protein complex
-native native.pdb                                      # A reference structure for RMSD calculations - MANDATORY!!!
-out:pdb_gz                                             # silent output flags
-out:file:silent_struct_type binary
-out:file:silent decoys.silent
-scorefile score.sc                                     # name of scorefile

If using multiple processes and no silent file:

-multiple_processes_writing_to_one_directory

Number of structures to produce (for demo):

-nstruct 5                                              # number of structures to produce

Number of structures to produce (for production run):

-nstruct 50000

FlexPepDock flags:

-flexPepDocking:lowres_abinitio
-flexPepDocking:pep_refine                              # Refine after ab-initio
-flexPepDocking:flexpep_score_only                      # add aditional interesting scores to scorefile

Packing flags:

-ex1
-ex2aro
-use_input_sc
-unboundrot native.pdb

Fragment picker flags:

-frag3 frags/frags.3mers.offset
-frag9 frags/frags.9mers.offset
-flexPepDocking:frag5 frags/frags.5mers.offset
-flexPepDocking:frag5_weight 0.25
-flexPepDocking:frag9_weight 0.1

Example Rosetta Command Line:

$PATH_TO_EXE/FlexPepDocking.release -database $PATH_TO_DB @flags

Overall protocol execution (demo):

  1. scripts/prep_abinitio.sh 2b1z (preparation step)

    This will create a 'frags' dir with frgments of the peptide for your run. This will also create links to the native.pdb, start.pdb and flags files from the input_files dir.

  2. prepack_example (prepacking step)

    This will create a start.ppk.pdb structure which is the pre-packed complex to start the simulation from. Also, a ppk.score.sc score file for the repacked structure, as well as a prepack.log log of the run.

  3. run_example (docking step)

    This will create the models of the interaction in a silent (compressed) file (5 for the demo, use 50,000 for real life problems) as well as an initial score file for the models.

  4. scripts/scoring/rescore.sh score.sc (rescoring step)

    This step is NOT needed if you use Rosetta version 3.3 onwards. If you use version 3.2, use this step to create a new score file (named 'newscore.sc') which includes the fpdock-abinitio recommended score for ranking and clustering of the models (reweighted_sc) as the last column. In this case, use 'newscore.sc' instead of 'score.sc' in the next step (clustering).

  5. scripts/clustering/cluster.sh [ntop] 2 score.sc native.pdb decoys.silent reweighted_sc (clustering step)

    This will cluster the [ntop] lowest energy models (use 5 in this demo, 500 for real life problems). The script relies on the specified score file 'score.sc' (use 'newscore.sc' if using Rosetta version 3.2), and ranks models according to the specified column 'reweighted_sc' (a reweighted version of the Rosetta score), with the specified clustering radius of 2A. The reprasentative models will be shown in the file 'clusters_by_reweighted_sc.txt', sorted by the score of their lowest-energy representatives.

Version

Latest version applies to svn revision 45531 (Oct 2011)

References

Raveh B, London N , Zimmerman L & Schueler-Furman O (2011) Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto their Receptors PLoS ONE 6(4): e18934.