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 Post subject: interaction table and HBplot
PostPosted: Mon Mar 01, 2010 7:16 am 

Joined: Thu Jan 28, 2010 5:59 am
Posts: 3
Hi,
Can you please let me know what is HBplot and what is the difference between the interactions in the interaction table and HBplot? Thanks, jes


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 Post subject: Re: interaction table and HBplot
PostPosted: Mon Mar 01, 2010 9:24 am 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 40
HB plot is the hydrogen-bonding network of a protein (see the reference on the HBplot tab; Bikadi et al., 2007). The axis represent the amino acid residues of the protein, a dot indicates if a hydrogen bond is present connecting two residues. From the HB plot secondary structure can be easily visualized. Moreover, bonds that contribute to 3D stability can be simply spotted as well. Amino acid residues that interact with the docked ligand are indicated on the right panel and on the plot as well.
The interaction table focuses on the detailed interaction of the docked ligand with residues of the protein.

I hope this helps- please let me know if you have further comments or questions.
Eszter


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 Post subject: Re: interaction table and HBplot
PostPosted: Thu Sep 06, 2012 10:20 pm 

Joined: Sun Jan 09, 2011 3:04 pm
Posts: 2
From your answer "Amino acid residues that interact with the docked ligand are indicated on the right panel and on the plot as well. " I assume that for each docking cluster several H-bonds that involve the ligand are observed.

My questions are the following:

1. Is there a way of telling the frequency (occupancy) of H-bond interactions (per residue)?

2. What is reported in the interactions table (H-bonds) often does not correspond to what is reported in HBplot. Can you please explain why?

3. What does "Other" mean in the Interactions Table?

Thanks in advance

George


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 Post subject: Re: interaction table and HBplot
PostPosted: Wed Aug 30, 2017 8:16 am 

Joined: Thu Jul 20, 2017 4:56 am
Posts: 6
Hi, thanks. Is it possible to get the interaction table between protein-ligand for runs other than the one with the lowest energy ? (Eg. largest surface area with higher energy)


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 Post subject: Re: interaction table and HBplot
PostPosted: Wed Aug 30, 2017 3:33 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 207
You can use the dropdown button at top right to see the interaction table for other results.


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