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Docking

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: 

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. 

 

Post Situation: 

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

Post Situation: 

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: 

Protein protein docking

Category: 
Docking

HI

I am performing a local docking using Rosie server for a complex obtained from patchdock. The residue names are checked as in Rosetta nomenclature. But strangely the resulting pdb shows a missing residue, that is the first residue of both the protomers are missing.  How is it possible or how to overcome it?

Post Situation: 

SnugDock: chain_id H represents more than one chain

Category: 
Docking

Hi,

I want to use snugdock in Rosie to model the binding structure between an antibody and an antigen. This is my input: http://rosie.rosettacommons.org/fs/46862/input/proteins.pdb

I get the following error message: 

Post Situation: 

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