General protein-protein docking when no info. on structure is availble

[Anonymous]

We plan to follow/advise the following steps for protein-protein docking when no known information on the complex structure is available and, it is necessary to do an initial global search around one partner. 

The objective of clustering is to, ideally, seek larger clusters of decoy structures having more closely spaced energies.

Hence, the following sequence of steps is proposed for protein-protein docking where no known information on structure is available:

1.  Generate many thousands of decoys using low_res_protocol_only in RosettaDock, and a global search over all space around fixed partner.

2.  Cluster this set and select highest scored structure from 1st of 2nd highest ranked cluster (check structure visually).

3.  Run high-resolution (docking_local_refine) RosettaDock with this selected structure as starting structure–generate 1000-10000 decoys.

4.  Cluster the high-resolution set and, again, select highest scored structure from 1st tor 2nd highest ranked cluster.

 

Any comments/additions to this sequence, would be welcomed.

Regards,

Jasnyderjr

[Anonymous]

I would suggest relatively more structures during the low-res phase, using computer time shifted from the high-res phase.  In my experience the high-res phase doesn’t change the inputs too much.  So I would do numbers more like:

100000 centroid decoys, filter down to 100-1000 or so, that both cover all the interesting binding modes AND cover the most interesting ones several structures deep, then run each of these through refinement 10-100 times.

I don’t think doing 1000 refinement docks on one centroid input will be more productive than running 100, and I’m not sure 100 is much better than 10.

[Anonymous]

I would suggest relatively more structures during the low-res phase, using computer time shifted from the high-res phase.  In my experience the high-res phase doesn’t change the inputs too much.  So I would do numbers more like:

100000 centroid decoys, filter down to 100-1000 or so, that both cover all the interesting binding modes AND cover the most interesting ones several structures deep, then run each of these through refinement 10-100 times.

I don’t think doing 1000 refinement docks on one centroid input will be more productive than running 100, and I’m not sure 100 is much better than 10.

[Anonymous]

I would suggest relatively more structures during the low-res phase, using computer time shifted from the high-res phase.  In my experience the high-res phase doesn’t change the inputs too much.  So I would do numbers more like:

100000 centroid decoys, filter down to 100-1000 or so, that both cover all the interesting binding modes AND cover the most interesting ones several structures deep, then run each of these through refinement 10-100 times.

I don’t think doing 1000 refinement docks on one centroid input will be more productive than running 100, and I’m not sure 100 is much better than 10.

[Anonymous]

I’ve sent this along to the RosettaDock maintainers for comment.

[Anonymous]

I’ve sent this along to the RosettaDock maintainers for comment.

[Anonymous]

I’ve sent this along to the RosettaDock maintainers for comment.

[Anonymous]

Thanks for the feedback.  I am required to ask this since I have been asked to verify with the RosettaDock community that I have set things up corectly.  We are experimenting with a protocol applicalble to protein complexes,  where only the structures of both (unbound) partners known separately.  Start wilth global search-low-resolutuon (LR), followed by obtainilng a smaller subset (eventual publilcation hopefully), then local refinement-high resolution (HR). The LR decoys are used as input to -docking_local_refine, are  all in centroid form, which the HR stage just rebuilds anyway–so I assume that’s ok.  Anyhow, I just would like to show the option flags and execution for both stages to verify I’m OK.  Thanks Again.

 

Low-Resoultion Global search:

-s lr.pdb

-ex1

-ex2aro

-native 1bj1.pdb

-docking:partners LH_VW

-nstruct 60

-docking:low_res_protocol_only

-randomize1

-randomize2

-mute core.util.prof ## dont show timing info

-out:file:scorefile lr.fasc

-mute core.io.database

-run:jran seed

-use_input_sc

-unboundrot 1bj1.pdb

-ignore_zero_occupancy false

-spin

 

/path/rosetta_bin_linux_2015.19.57819_bundle/main/source/bin/docking_protocol.default.linuxgccrelease  @flags -database /path/rosetta_bin_linux_2015.19.57819_bundle/main/database -run:constant_seed  > log_decoy

where different value is assigned for seed for each of thousands of LR decoys

High-Resolution Local perturbations (MC):

-ex1

-ex2aro

-native input/1bj1.pdb

-docking:partners LH_VW

#-dock_pert 3 8

-docking_local_refine

-nstruct 1000

-spin

-mute core.util.prof ## dont show timing info

-out:file:fullatom #output in fullatom scorefile

-out:file:score_only

-out:path:score docking_hr

-mute core.io.database

-use_input_sc

-unboundrot input/1bj1.pdb

/path/ROSETTA_3.4/rosetta_bin_linux_2015.19.57819_bundle/main/source/bin/docking_protocol.default.linuxgccrelease  -s docking_hr/lr_decoy.pdb @flags_hr -out:file:scorefile score_decoy.fasc -database /path/ROSETTA_3.4/rosetta_bin_linux_2015.19.57819_bundle/main/database >docking_hr/log_decoy

decoy is assigned integer.

The only thing I notice, is that disulfides are not being recognized, as I just get 0.00 for the dslf_ terms in the HR log files.  I can remedy this using the -in:fix_disulf disulfides

command with disulfides being a file listing the pairs of Cys residues that form disulfides, then and see  lines like “Fixing a disulfide between 23 and 87”,  and output pdbs ( if selected) with Cys HG not present.

Thanks Again.

jasnyderjr

 

 

[Anonymous]

Thanks for the feedback.  I am required to ask this since I have been asked to verify with the RosettaDock community that I have set things up corectly.  We are experimenting with a protocol applicalble to protein complexes,  where only the structures of both (unbound) partners known separately.  Start wilth global search-low-resolutuon (LR), followed by obtainilng a smaller subset (eventual publilcation hopefully), then local refinement-high resolution (HR). The LR decoys are used as input to -docking_local_refine, are  all in centroid form, which the HR stage just rebuilds anyway–so I assume that’s ok.  Anyhow, I just would like to show the option flags and execution for both stages to verify I’m OK.  Thanks Again.

 

Low-Resoultion Global search:

-s lr.pdb

-ex1

-ex2aro

-native 1bj1.pdb

-docking:partners LH_VW

-nstruct 60

-docking:low_res_protocol_only

-randomize1

-randomize2

-mute core.util.prof ## dont show timing info

-out:file:scorefile lr.fasc

-mute core.io.database

-run:jran seed

-use_input_sc

-unboundrot 1bj1.pdb

-ignore_zero_occupancy false

-spin

 

/path/rosetta_bin_linux_2015.19.57819_bundle/main/source/bin/docking_protocol.default.linuxgccrelease  @flags -database /path/rosetta_bin_linux_2015.19.57819_bundle/main/database -run:constant_seed  > log_decoy

where different value is assigned for seed for each of thousands of LR decoys

High-Resolution Local perturbations (MC):

-ex1

-ex2aro

-native input/1bj1.pdb

-docking:partners LH_VW

#-dock_pert 3 8

-docking_local_refine

-nstruct 1000

-spin

-mute core.util.prof ## dont show timing info

-out:file:fullatom #output in fullatom scorefile

-out:file:score_only

-out:path:score docking_hr

-mute core.io.database

-use_input_sc

-unboundrot input/1bj1.pdb

/path/ROSETTA_3.4/rosetta_bin_linux_2015.19.57819_bundle/main/source/bin/docking_protocol.default.linuxgccrelease  -s docking_hr/lr_decoy.pdb @flags_hr -out:file:scorefile score_decoy.fasc -database /path/ROSETTA_3.4/rosetta_bin_linux_2015.19.57819_bundle/main/database >docking_hr/log_decoy

decoy is assigned integer.

The only thing I notice, is that disulfides are not being recognized, as I just get 0.00 for the dslf_ terms in the HR log files.  I can remedy this using the -in:fix_disulf disulfides

command with disulfides being a file listing the pairs of Cys residues that form disulfides, then and see  lines like “Fixing a disulfide between 23 and 87”,  and output pdbs ( if selected) with Cys HG not present.

Thanks Again.

jasnyderjr

 

 

[Anonymous]

Thanks for the feedback.  I am required to ask this since I have been asked to verify with the RosettaDock community that I have set things up corectly.  We are experimenting with a protocol applicalble to protein complexes,  where only the structures of both (unbound) partners known separately.  Start wilth global search-low-resolutuon (LR), followed by obtainilng a smaller subset (eventual publilcation hopefully), then local refinement-high resolution (HR). The LR decoys are used as input to -docking_local_refine, are  all in centroid form, which the HR stage just rebuilds anyway–so I assume that’s ok.  Anyhow, I just would like to show the option flags and execution for both stages to verify I’m OK.  Thanks Again.

 

Low-Resoultion Global search:

-s lr.pdb

-ex1

-ex2aro

-native 1bj1.pdb

-docking:partners LH_VW

-nstruct 60

-docking:low_res_protocol_only

-randomize1

-randomize2

-mute core.util.prof ## dont show timing info

-out:file:scorefile lr.fasc

-mute core.io.database

-run:jran seed

-use_input_sc

-unboundrot 1bj1.pdb

-ignore_zero_occupancy false

-spin

 

/path/rosetta_bin_linux_2015.19.57819_bundle/main/source/bin/docking_protocol.default.linuxgccrelease  @flags -database /path/rosetta_bin_linux_2015.19.57819_bundle/main/database -run:constant_seed  > log_decoy

where different value is assigned for seed for each of thousands of LR decoys

High-Resolution Local perturbations (MC):

-ex1

-ex2aro

-native input/1bj1.pdb

-docking:partners LH_VW

#-dock_pert 3 8

-docking_local_refine

-nstruct 1000

-spin

-mute core.util.prof ## dont show timing info

-out:file:fullatom #output in fullatom scorefile

-out:file:score_only

-out:path:score docking_hr

-mute core.io.database

-use_input_sc

-unboundrot input/1bj1.pdb

/path/ROSETTA_3.4/rosetta_bin_linux_2015.19.57819_bundle/main/source/bin/docking_protocol.default.linuxgccrelease  -s docking_hr/lr_decoy.pdb @flags_hr -out:file:scorefile score_decoy.fasc -database /path/ROSETTA_3.4/rosetta_bin_linux_2015.19.57819_bundle/main/database >docking_hr/log_decoy

decoy is assigned integer.

The only thing I notice, is that disulfides are not being recognized, as I just get 0.00 for the dslf_ terms in the HR log files.  I can remedy this using the -in:fix_disulf disulfides

command with disulfides being a file listing the pairs of Cys residues that form disulfides, then and see  lines like “Fixing a disulfide between 23 and 87”,  and output pdbs ( if selected) with Cys HG not present.

Thanks Again.

jasnyderjr

 

 

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