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Docking

Use NMR ensemble in protein-protein docking?

Submitted by cossio on Sun, 2015-09-13 07:57
Category: 
Docking

I want to dock two proteins, A and B. I have pdb files for both of them, A.pdb and B.pdb. Now, A.pdb is an X-ray structure, while B.pdb is an NMR ensemble. Is it possible to run a docking simulation with these inputs? How can I do it?

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Rosetta 3 - Applications

Fnat and Irms are nan in score.sc from docking_protocol?

Submitted by cossio on Sun, 2015-09-13 07:34
Category: 
Docking

I am running a docking_protocol for two proteins. Inspecting the score.sc file, I find that the columns Fnat and Irms are "nan" (Not A Number, I suppose). Why could this be happening? I can post more details if needed.

(BTW, what does Fnat mean?)

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Rosetta 3 - Applications

Antibody Docking application

Submitted by Maryam_tabasinezhad on Sat, 2015-09-05 09:58
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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Rosetta 3 - Applications

InterfaceAnalyzer dSasa calculation

Submitted by mintseris on Wed, 2015-09-02 09:43
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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Rosetta 3 - Applications

How to improve ROSIE docking2 results?

Submitted by AdoCbl on Sun, 2015-08-09 01:22
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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ROSIE - General

RMSD values in docking2 and symmetric_docking runs

Submitted by AdoCbl on Sun, 2015-08-09 00:48
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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ROSIE - General

docking2: local_docking vs docking_local_refine

Submitted by AdoCbl on Sat, 2015-08-08 23:57
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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