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Docking

DockingProtocol mover ensemble error

Category: 
Docking

Hi all,

I would like to know if the mover DockingProtocol allows the use of ensemble for running docking with RosettaScripts.

I have an ensemble for both protein partners and I have used the flags -ensemble1 and -ensemble2.

If I use the DockingProtocol mover (script file test1.xml attached) aparently it does not turn ON the ensemble flag and I get an unexplained error:

 

...

Post Situation: 

Negative Design

Category: 
Docking

Hello,

 

I am trying to come up with a protocol (xml script) that will allow me to perform positive design for one substrate and negative design for the inhibitor. Our goal is to create a protein that maintains functionality and is resistant to the inhibitor.

I am open to any suggestion. I have not been able to find any documentation on how to perform docking_design in this manner.

Thanks

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How to define the surface (???.surf) for surface_docking?

Category: 
Docking

Dear Rosetta Team,

When docking a protein with a solid surface, Rosetta will need a .surf file; Any one can tell me how to setup/edit a .surf file for a certain solid surface (a .pdb file) for surface docking? In the demo example for the calcite.surf, there is not detailed instruction to tell how to do it? Only three lines, with likely X,y,z in the calcite.surf file. I dont know what they are representing for a solid surface?

Thanks

An Pu

Post Situation: 

Fluctuations in I_sc

Category: 
Docking

Hello,

I am using "local  refinement" to calculate the I_sc of protein complexes. When I ran Rosetta for the exact same structure multiple times and I got a significant fluctuation in I_SC score, ranging from -2 to -15. This means that in one trial, the complex is unfavorable, but it is favorable in the subsequent trial. What is the reason for this? How can I overcome it? 

Thank you in advance,

Emine

Post Situation: 

Flexpepdock I_hb scoring term

Category: 
Docking

I am attempting to dock a peptide onto a protein using flexpepdock. The docking completes and the identified structures are plausible solutions. However, when I examine the score.sc file, I notice that the I_hb term has a single, extremely high value for all structures:

I_hb = 18446744073709551616.000

I am prepacking the structure before docking:

FLEXPEP -s PEPTIDE.pdb -flexpep_prepack -ex1 -ex2aro -overwrite

FLEXPEP -s PEPTIDE_0001.pdb -pep_refine -ex1 -ex2aro -nstruct 100 -lowres_preoptimize -native PEPTIDE_0001.pdb

Post Situation: 

PDB moves after relaxing

Category: 
Docking

Dear all,

I am starting to learn Rosetta right now and have to relax a structure before I learn more because of a deadline. 

After I run the Rosetta Relax successfully when I load the result in Chimera, the pdb seems to be off from the density by a little bit. But when I fit it in, it looks better. 

Is this normal? Or am I doing something wrong?

(My structure has multiple repeats of the same unit and I am only fitting one of them)

Best,

Hamid

Post Situation: 

Question about FlexPepDock score

Category: 
Docking

Hey all! I just have a couple of questions:

01. In FlexPepDock, what does the interface score (I_sc) correspond to? The interface between the receptor and peptide? Or is it something else?

02. Can the interface score be used to evaluate the strength of binding between the receptor and peptide? If not, how can I evaluate the said parameter?

Thank you very much! Cheers!

Post Situation: 

Why I_sc of Rosetta 2016.02 and 2018.21 are so different?

Category: 
Docking

Hello,

I was using Rosetta 2016.02 "local  refinement" to calculate the interface scores of known protein complexes (in a bound form).

Now, I tried docking the same protein complexes, with exactly the same flags with Rosetta 2018.21. I realized that the content of the score file has changed and it gives totally different I_sc and total_score.  Almost any protein complex that I tried gives favorable results now (i.e. I_sc < -5).  Why is this the case? 

I couldn't find what has changed since 2016.02 version. 

Post Situation: 

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