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PostPosted: Wed Jul 10, 2013 9:19 am 
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Dear All,

Hello, I am very new in this molecular docking field. Currently, I am using Autodock Vina with PyRx Virtual Screening Tool.

In my project, I am doing a screening for hypothetical protein which have potential sugar binding affinity. Based on my given organism, I found a few potential proteins and had proceed with protein modelling and followed by docking with a panel of different sugar molecules.

When I was presenting my results in a seminar, the examiner asked me a few questions which I was told I had answered incorrectly, and they want me to find out the answers myself without giving a clue where to find out about it.

The first question was for Binding Affinity: While I understand the more negative the binding affinity, the stronger the binding, however, I couldn't answer what is the acceptable energy values where it is significant to show binding occurred. Eg: Is -4.0 good enough, or should be -8.0 and above? Is there any cut-off?

For the part for "analysis results", there are: Binding Affinity (kcal/mol); mode; RMSD lower bound and RMSD higher Bound. If I were to analyse my docking results, how does Binding Affinity relates to RMSD?

My Google search points me to this website:
http://autodock.1369657.n2.nabble.com/A ... 42242.html
However, I couldn't understand most part of discussions. I try to read up the manual but doesn't explain much in this aspect.

Is there any reading or references that I can refer to?

Very sorry for my bad English as I am not a native speaker.


Thank you for your help in advanced.

Cheers, and have a good day.


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PostPosted: Tue Jul 30, 2013 12:06 am 
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No body can advice or help?

:cry: :(


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PostPosted: Wed Feb 25, 2015 2:20 pm 
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adriankoh wrote:
No body can advice or help?

:cry: :(


I guess you're alone. on your own you will have to earn
http://www.parakazanma-yollari.com/


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