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Docking

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

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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!

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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. 

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Error while converting mol2 to params using molfile_to_params.py

Category: 
Structure prediction
Docking
Design

I'm trying to run python /home/labusr/rosetta/main/source/scripts/python/public/molfile_to_params.py --keep-names --clobber --extra_torsion_output --centroid gtp.mol2 -p GTP -n GTP, on a gtp.pdb that has been reduced using phenix.reduce and converted to mol2 using openbabel. Below is the error I get. 

 

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The question of ligand docking with constraints

Category: 
Docking

Hello,

I read the paper Rosetta and the Design of Ligand Binding Sites

and it enlightens me.

According to the method of this paper,  I design my enzyme.

However,  I find these are a few unreasonable results which show reaction atom of ligand  do not close to  catalytic triad,

but  the opposite side of ligand close to  catalytic triad.

So I want to  make docking with  constraints

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solution of the length of peptide candidates is larger than substrate with FlexPepDock and Flexpepbind

Category: 
Docking

Hi all,

I'm trying to dock some peptide candidates to a pocket. The pocket of template complex has a 6 aa length peptide , XXXpSXXX. But my peptide candidates I would like to dock is 7 aa length, XXXXXSXX. As you see, the phosphorylation site between substrate and docking peptide don't match on the same position.

My question is

1. Will it be a matter of the enenry score (specially I_sc, pep_sc, etc) if the peptide I would like to dock is longer than the template? if yes, what's the best solution for this case?

Post Situation: 

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