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Docking

Hydrogen bond detection and shape complementarity

Category: 
Docking

HI,

I have PDB strucures of antigen- antibody complexs. want to studythe hydrogen bond pattern at the ineterface and also the shape complimentarity. As per the following manuscript (Kuroda et al, (2016) Bioinformatics, 32(16):2451-2456) the command line

report_hbonds_for _plugin.linuxgccrelease

-s

-prevent packing true

sc.linuxgccrelease

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Docking results

Category: 
Docking

hi

I am docking an antibody to antigen using the snugdock server. Just wanted to know whtat is the reference structure in the the RMSD deviation in the score.sf files. Is it the structure with the lowest rosetta energy. In case if you want to compare the original structure of complex with decoy structure what is the easiest option. i am attaching the gnuplot out put of the Total Score Vs RMSD  . Any help would highly be appreciated

Dr. Suji george

   

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How can I set ref2015 and ligand.wts(-restore_pre_talaris_2013_behavior )

Category: 
Docking

Hello, I want to design my protein wit XML script as the paper  Rosetta and the Design of Ligand Binding Sites
 

I want to dock with ligand.wts(-restore_pre_talaris_2013_behavior

and design protein with ref2015.wts.

But the option -restore_pre_talaris_2013_behavior seem to have impact in ref2015.wts.

How can I solve it?

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SnugDocking result interpretation

Category: 
Docking

Hi there:

I use snugDocking to Dock different antibody- antigens.  I wonder how could I determine good binding vs bad binding from the result web page.

I am currently decide by look at 1. interface score 2, similarity of top 10 models.  If the interface score is low and top 10 models have a couples model in similar position, I assume it is good binding, otherwise It isn't

give an example:

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Sampling a wider range of RMSD of poses by Rosetta Dock

Category: 
Docking

Hi, I am designing a protein interface of a nanobody with my target antigen.

1000 initial poses were generated by patchdock and 1000 designs were generated per each pose.

After ploting the ddg-rmsd scatter plot, I found all the poses has a characteristic scatter plot like fig. A attached (a narrow RMSD range within ~0.25A, while a majority stays exactly at 0.00A).

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script recommendations? for high res docking from low res

Category: 
Docking

Hi:

Is there a rosetta or pyrosetta script  (or general protocol) you would recommend for a pdb that already has a small molecule ligand docked in a low resolution docking model?

I used Zhang lab's BP Slim server to get this lo res docking, and now what I need to do is refine that model to high res, atomic scale.

 

thank you all so much, I am learning rapidly from this most generous and helpful community.  - Amy

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missing atom number 5 atom name CB

Category: 
Docking

I am contacting you because I am getting an error in results with Rosetta. Successfully finished protein-protein docking. I can see in the output that following lines complaining about missing atoms. I have prepared protein in ICM, Molsoft. I checked the input file those I have given as input.pdb, there were no missing any CB atoms in all amino acid. Docking finished successfully and generated score value. Do you think this missing atom will make any impact in score value? Let me know how can solve this problem. 

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