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Docking

Antibody Docking application

Category: 
Docking

Hi, 

I want to do docking antibody-antigen complex. Understanding from literature, ensemble docking and snug dock is better for Ab-ag. But I didn’t find a complete tutorial or documentation for snug dock. I found just the page in the following link that is some confusing:

https://www.rosettacommons.org/docs/latest/application_documentation/antibody/snugdock

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InterfaceAnalyzer dSasa calculation

Category: 
Docking

Hi,

I had previously run InterfaceAnalyzer in Rosetta 3.5 but then had to re-run it with a more recent version (2015.19.57819) and was surprised to notice that the dSASA numbers were quite a bit different. This is not a calculation I expected to change much and it shouldn't depend on scoring functions.

I just ran the following on 1brs in the integration tests folder:

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How to improve ROSIE docking2 results?

Category: 
Docking

ROSIE docking2 and symmetric_docking runs both give plots
and spreadsheets containing many columns of data.
Which spreadsheet columns best reflect the quality of a run?
Should the best runs have each plot with a narrow funnel on the left
and a rather wide flat plateau to the right?
Should there be very few points scattered above or below the plateau?

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RMSD values in docking2 and symmetric_docking runs

Category: 
Docking

I am curious how ROSIE docking2 and symmetric_docking runs determine RMSD values.

For docking2 runs, are RMSD values determined between
the output\trigger_00001.dock\native.pdb file
and each output\trigger_00001.dock\proteins_*.pdb file?
If so, how is the native.pdb file made?
Is it a weighted average of all the proteins_*.pdb files
with more weight given to files with better scores or I_sc values?

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docking2: local_docking vs docking_local_refine

Category: 
Docking

When I submit ROSIE docking2 jobs at http://rosie.rosettacommons.org/docking2/submit
there are options for local_docking and docking_local_refine docking protocols.
What is the difference between these options?
Where can I find documentation about them?

Thanks!

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How to judge docking success for two proteins without knowledge of native structure

Category: 
Docking

If you are trying to dock two proteins, using a global search, with no knowledge of correct answer (native structure) , how does one judge a docking success?. When reporting benchmark results, for example, the native (or mock-native) structure is used to rmsd against, and the definition of docking funnel is based on I_rmsd, so judgement of docking success is always based on some known (native) structure (or correct answer). Starting with just two proteins arbitrarily place apart.

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Cancel / delete Rosie not working

Category: 
Docking

Hi,

I am trying to Delete / Cancel jobs on Rosie that I suspect will fail, so I want to save running time and send another job.

But when I click on the Delete / Cancel links on my account fglaser_rosie, nothing happens....

What I am doing wrong?

Best regards,

Fabian
Technion, Haifa
Israel

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Job 「№15623」has failed

Category: 
Docking

Hi

Iam a newby with Rosie, I sent a PDB and sdf file with many molecules for Rosie docking, and I got the following input error message:

Job 「№15623」has failed with the message:

molfile_to_params step failed, please double check your input files!

I searched the documentation and for what I know the input PDB and the SDF where in correct format, but of course I maybe wrong...

Could you please explain me what exactly is wrong with the input and how to correct it?

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