vadiraj kurdekar vadirajgcppc at
Fri Dec 27 02:53:56 PST 2013

1. docking only predicts only binding.  a inhibitor and activator both binds to the receptor stronger the binding stronger the activity. therefore docking scores only tells you whether a molecule is strong binder or weak binder not they are activator or inhibitor
2. higher the score i.e. more the negative the value (delta G) more stronger it binds.
3. in autodock the pose that is repeated several times or else low energy binding pose.
4. binding energy differes from target to target there is no fixed rule regarding how much docking score is needed for strong activity we can just compare with standard ligand.
5. bumps are clashes. bumps are not good
6. binding energy increases with increased no of Hbonds. pose with more no of Hbonds are generally good

With Regards,
Vadiraj Kurdekar,
Research Scholar, Pharmacy Dept.,
Birla Institute of Technology and Science-Pilani,
Pilani Campus, 
Rajasthan, PIN: 333031
Mobile: + 91 9460763664


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On Thursday, 26 December 2013 11:48 PM, vishalshounik <vishalshounik at> wrote:
1.How can I understand that my ligand is activator or inhibitor after docking?

2.How to interpret Docking results?
3.After&nbsp; docking process, I have find several poses&nbsp; 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&nbsp; 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 ?

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