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Question about FlexPepDock score
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?
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.
Question on restraining receptor symmetry when docking ligand
Hi there,
Is there a way to maintain receptor symmetry when performing flexible ligand docking protocol?
Thanks,
Subha
antibody-antigen interface score
Hi:
for example I got antibody- antigen interface score -10.650, how about -6.345
Is it indicate good binding?
Is the interface score related to Kcal/mol ?
Thanks a lot
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Error while converting mol2 to params using molfile_to_params.py
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.
The question of ligand docking with constraints
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
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?
Docking a ligand to two movable domains of a protein
I have a scenario where a protein is composed of two domains (its actually two chains, but I can make it a single chain) for Rosetta's purposes.
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Protein protein 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?
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