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 Post subject: Inhibitor vs activator
PostPosted: Wed Aug 08, 2012 9:25 am 

Joined: Thu Jul 05, 2012 8:20 am
Posts: 2
Hello,

I have a question concerning a results interpretation:
I am docking several ligands to one kinase in order to find inhibitory or activating molecules. When I compare the Kd's of the different ligands, normalized to my natural substrate, I find some results smaller or bigger than 1 (1 stands for the Kd of the substrate). Given that the Kd < 1 results reflect the potency of inhibition (known kinase inhibitor show the most effective - < 1 - results), is it valid to interpret the outcomes with a Kd > 1 as activators?

Thank you for your help
Best, Robert


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 Post subject: Re: Inhibitor vs activator
PostPosted: Thu Aug 09, 2012 12:29 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 40
Hello,

I think it is a bit too speculative, but I am not expert in the field of kinases - but being an activator is I think not only a Kd issue.

Kind Regards,
Eszter


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 Post subject: Re: Inhibitor vs activator
PostPosted: Mon Dec 23, 2013 8:47 am 

Joined: Mon Dec 23, 2013 8:33 am
Posts: 2
PREACT_Docking1 wrote:
Hello,

I have a question concerning a results interpretation:
I am docking several ligands to one kinase in order to find inhibitory or activating molecules. When I compare the Kd's of the different ligands, normalized to my natural substrate, I find some results smaller or bigger than 1 (1 stands for the Kd of the substrate). Given that the Kd < 1 results reflect the potency of inhibition (known kinase inhibitor show the most effective - < 1 - results), is it valid to interpret the outcomes with a Kd > 1 as activators?

Thank you for your help
Best, Robert


Robert can you help me with below queries?

1.How can I understand that my ligand is activator or inhibitor after docking?

2.How to interpret Docking results?

3.After docking process, I have find several poses which pose i need to consider and which binding energy values i can say are the best binding ?along with energy values am i need to consider any another factors?

4.Are there any binding energy Ranges Values ,As i can say it is agonist or antagonist?
5.What is Bump what are the advantages of Bumps after docking ?If there are more bumps after docking how to conclude?at the same time less bumps?

6.Significance of More hydrogen bonds and less hydrogen bonds and length of the hydrogen bonds also plays roles in best binding pose or binding energy after docking ?


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 Post subject: Re: Inhibitor vs activator
PostPosted: Wed Feb 25, 2015 7:49 am 

Joined: Wed Feb 25, 2015 7:39 am
Posts: 1
am docking several ligands to one kinase in order to find inhibitory or activating molecules. When I compare the Kd's of the different ligands, normalized to my natural substrate, I find some results smaller or bigger than 1 (1 stands for the Kd of the substrate). Given that the Kd < 1 results reflect the potency of inhibition (known kinase inhibitor show the most effective - < 1 - results), is it valid to interpret the outcomes with a Kd > 1 as activators?

Thank you for you


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 Post subject: Re: Inhibitor vs activator
PostPosted: Wed Feb 25, 2015 10:35 am 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 204
You just can say that it seems that the interactions are stronger or weaker, you should investigeta the atomic interactions and compare with known activators and inhibitors to decide about your problem, docking energy itself is not enough alone.

markjon55 wrote:
am docking several ligands to one kinase in order to find inhibitory or activating molecules. When I compare the Kd's of the different ligands, normalized to my natural substrate, I find some results smaller or bigger than 1 (1 stands for the Kd of the substrate). Given that the Kd < 1 results reflect the potency of inhibition (known kinase inhibitor show the most effective - < 1 - results), is it valid to interpret the outcomes with a Kd > 1 as activators?

Thank you for you


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