homo-oligomeric proteins………….folddock+symmetry+abinito

[Anonymous]

Hello everyone,

I a looking forward to generate a homodimeric protein using rosetta abinitio with the help of fold and dock and symmetry definition files.

(ref to:Das R, André I, Shen Y, Wu Y, Lemak A, Bansal S, Arrowsmith CH, Szyperski T,
Baker D. Simultaneous prediction of protein folding and docking at high resolution. Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):18978-83)

My command line option was:

/home/chaos/Download/ROSETTA/v3.1/rosetta_source/bin/AbinitioRelax.linuxgccdebug
-run:protocol broker
-broker:setup setup_init.tpb
-out:nstruct 5
-out:file:scorefile score.fsc
-database /home/chaos/Download/ROSETTA/v3.1/rosetta_database
-in:file:fasta ../3vubq.fasta
-symmetry:symmetry_definition ../sym_def_dimer.dat1
-in:file:frag9 ../ff3vuba09_05.200_v1_3
-in:file:frag3 ../ff3vuba03_05.200_v1_3
-out:pdb
-out:file:silent OUT_3vub
-out:file:silent_struct_type binary
-relax:fast
-relax:jump_move
-symmetry:initialize_rigid_body_dofs
-fold_and_dock::rotate_anchor_to_x
-rg_reweight 0.01
-run:reinitialize_mover_for_each_job

The protein is a dimer i.e 101 reidues in each monomer. I tried using 3vub (fasta file) with one monomeric chain and fragment library for the 101 residues (monomer). Sine, the symmetry definitions are defined, I should be able to generate a dimeric structure after the run. But, the run generates a monomeric structure. When I try using a fasta file of a dimer and fragment library for a monomer, I do not get the structure of the other monomer, since, the fragment file doesn’t contain any details about it. I shall be thankful if helped with any solution towards this.

Thanking you,
Anusmita

[Anonymous]

I’ve pointed this question out to one of the authors, hopefully they’ll be able to reply.

[Anonymous]

Hi,

I have the same predicament. Have you found an answer you could share?

thanks.

> Hello everyone,
>
> I a looking forward to generate a homodimeric protein using rosetta abinitio with the help of fold and dock and symmetry definition files.
>
> (ref to:Das R, André I, Shen Y, Wu Y, Lemak A, Bansal S, Arrowsmith CH, Szyperski T,
> Baker D. Simultaneous prediction of protein folding and docking at high resolution. Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):18978-83)
>
> My command line option was:
>
> /home/chaos/Download/ROSETTA/v3.1/rosetta_source/bin/AbinitioRelax.linuxgccdebug
> -run:protocol broker
> -broker:setup setup_init.tpb
> -out:nstruct 5
> -out:file:scorefile score.fsc
> -database /home/chaos/Download/ROSETTA/v3.1/rosetta_database
> -in:file:fasta ../3vubq.fasta
> -symmetry:symmetry_definition ../sym_def_dimer.dat1
> -in:file:frag9 ../ff3vuba09_05.200_v1_3
> -in:file:frag3 ../ff3vuba03_05.200_v1_3
> -out:pdb
> -out:file:silent OUT_3vub
> -out:file:silent_struct_type binary
> -relax:fast
> -relax:jump_move
> -symmetry:initialize_rigid_body_dofs
> -fold_and_dock::rotate_anchor_to_x
> -rg_reweight 0.01
> -run:reinitialize_mover_for_each_job
>
>
> The protein is a dimer i.e 101 reidues in each monomer. I tried using 3vub (fasta file) with one monomeric chain and fragment library for the 101 residues (monomer). Sine, the symmetry definitions are defined, I should be able to generate a dimeric structure after the run. But, the run generates a monomeric structure. When I try using a fasta file of a dimer and fragment library for a monomer, I do not get the structure of the other monomer, since, the fragment file doesn’t contain any details about it. I shall be thankful if helped with any solution towards this.
>
> Thanking you,
> Anusmita

[Author]

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