Jump to content

  • Log in with Facebook Log in with Twitter Log in with Windows Live Log In with Google      Sign In   
  • Create Account

Submit your paper to J Biol Methods today!
Photo
- - - - -

Autodock Vina Results: Binding Affinity (Kcal/mol)


  • Please log in to reply
1 reply to this topic

#1 Adrian K

Adrian K

    Legendary Graduate Beggar

  • Global Moderators
  • PipPipPipPipPipPipPipPipPipPip
  • 708 posts
28
Excellent

Posted 08 July 2013 - 11:32 PM

Dear All,
First of all, I am very new in molecular docking field.
I am using Autodock Vina with PyRx Virtual Screening Tool.

For the part for "analysis results", there are: Binding Affinity (kcal/mol); mode; RMSD lower bound and RMSD higher Bound.

The question is:
1) if I were to analyse my docking results, how does Binding Affinity relates to RMSD?
2) I understand that the lower the binding affinity, the stronger the ligand bind to the protein. However, is there any energy values that we can consider it "significant" or strong? For example, is binding energy -2.0 is strong enough, or it must be -8.0 or -5.0 and above? This is because I do not find it in any of the manual.

Thank you for your help in advanced.

Cheers.
Expecting the world to treat you fairly because you are a good person is like expecting the lion not to attack you because you are a vegetarian.

..."best of our knowledge, as far as we know this had never been reported before, though I can't possible read all the published journals on earth, but by perform thorough search in google, the keywords did not match any documents"...

"what doesn't kill you, makes you stronger"---Goddess Casandra reminds me to be strong

"It's all just DNA. Do it."---phage434

#2 Inbox

Inbox

    Veteran

  • Active Members
  • PipPipPipPipPipPipPipPipPipPip
  • 329 posts
21
Excellent

Posted 09 July 2013 - 11:38 PM

More the negative value more better indicator it is. below -1 it should be ok. u have to select most Negative one.

note.- I asked my friend about it, he told me so. I used autodock once or twice only, if I will know more I will let u know.

Edited by prabhubct, 09 July 2013 - 11:39 PM.





Home - About - Terms of Service - Privacy - Contact Us

©1999-2013 Protocol Online, All rights reserved.