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: MEMBRANES STRUCTURE_PREDICTION Author: Vladimir Yarov-Yarovoy

Modified version of membrane relax protocol that uses centroid based Menv_smooth term (membrane specific residue environment) derived from updated database of membrane protein structures.

Running the protocol capture

Standard relax protocol flags:

-relax:fast
-relax:constrain_relax_to_start_coords
-relax:default_repeats 2
-in:file:fullatom
-in:file:native input/BRD4.pdb
-s input/BRD4.pdb
-nstruct 1
-out:file:silent_struct_type binary
-out:file:silent Menv_smooth-BRD4_frlx.out
-mute core.util.prof
-mute core.io.database
-run:no_prof_info_in_silentout
-out:file:scorefile Menv_smooth_score.sc

Transmembrane regions prediction input:

-in:file:spanfile input/BRD4.span

Menv_smooth-membrane-relax protocol specific weights:

-score:weights membrane_highres_Menv_smooth.wts

Membrane normal and membrane center search options:

-membrane:normal_cycles 40
-membrane:normal_mag 15
-membrane:center_mag 2

Example Rosetta Command Line:

./bin/relax.linuxiccrelease \
    -relax:fast \
    -relax:constrain_relax_to_start_coords \
    -relax:default_repeats 2 \
    -in:file:fullatom \
    -in:file:native input/BRD4.pdb \
    -in:file:spanfile input/BRD4.span \
    -s input/BRD4.pdb \
    -score:weights membrane_highres_Menv_smooth.wts \
    -membrane:normal_cycles 40 \
    -membrane:normal_mag 15 \
    -membrane:center_mag 2 \
    -nstruct 1 \
    -out:file:silent_struct_type binary \
    -out:file:silent Menv_smooth-BRD4_frlx.out \
    -mute core.util.prof \
    -mute core.io.database \
    -run:no_prof_info_in_silentout \
    -out:file:scorefile Menv_smooth_score.sc \

Version

If checked into trunk, SVN revision number: 39837

Other Comments

Membrane relax protocol specific input file (BRD4.span in the above example) generated using OCTOPUS transmembrane regions prediction server (http://octopus.cbr.su.se/) and Menv_smooth-membrane-relax/script/octopus2span.pl script as follows:

Menv_smooth-membrane-relax/script/octopus2span.pl BRD4.octopus

where BRD4.octopus is OCTOPUS topology file gererated by the server.

Sample OCTOPUS topology file:

##############################################################################
OCTOPUS result file
Generated from http://octopus.cbr.su.se/ at 2008-09-18 21:06:32
Total request time: 6.69 seconds.
##############################################################################


Sequence name: BRD4
Sequence length: 123 aa.
Sequence:
PIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFV
WWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGA
GIV

OCTOPUS predicted topology:
oooooMMMMMMMMMMMMMMMMMMMMMiiiiMMMMMMMMMMMMMMMMMMMMMooooooMMM
MMMMMMMMMMMMMMMMMMiiiiiiiiiiiiiiiiiiiiiMMMMMMMMMMMMMMMMMMMMM
ooo

Sample span file generated by Menv_smooth-membrane-relax/script/octopus2span.pl:

TM region prediction for BRD4 predicted using OCTOPUS
4 123
antiparallel
n2c
   6    26     6    26
  31    51    31    51
  58    78    58    78
  97   117    97   117
  • 1st line is comment line.
  • 2nd line shows number of predicted transmembrane helices (4 in the example above) and total number of residues (123 in the example above).
  • 3rd line shows predicted topology of transmembrane helices in the membrane (currently only antiparallel topology is implemented).
  • 4th line and all lines below show start and end residue numbers of each of the predicted transmembrane helices (current format repeats these numbers twice).