Eric di Luccio
Stardust and other Intergalactic considerations
08.25
2010

by Eric

in science

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Virtual ligand screening

There are many cool things that can be done when mixing wet “classical” biochemistry and computational biology/biophysics. The virtual ligand screening is one of those things that fall into the major cool category. Nowadays computer have plenty of horsepower that can be put into good use to simulate the binding of libraries of small molecules onto an active site of an enzyme for instance. Following the in silico simulations, the *best* molecules are assessed in the lab for their *experimental* binding/inhibitory properties. In the following video, I used AutodockVina to dock a small subset of 943 compounds into the human SETD1 (NSD1): 20 best docking solutions for each compounds = 18860 docking solutions!

2 Responses to “Virtual ligand screening”

#1

Carlos Ortega

Greetings!
I like the AutoDock Vina Program because is easy to use and I think that this program is good!!!
I am doing a VS too, and I can see many interesting things.
In your VS which molecule did you choose? and why?
Did you realice the experiment with this molecule?
Is correlationed the affitiy score with the experimental binding?
Pardon with my english, I am learning.
Thanks!

#2

Eric

Hi Carlos,

For this video, I used a model I build of the histone methyl transferase region (SET domain) of NSD1. NSD1 is one of the transcriptional co-regulator that is being investigated in my lab (http://webbuild.knu.ac.kr/~diluccio/). So far, the relative docking affinities predicted by AutoDock Vina appear to “agree” with the experimental binding. It is always good when computational biology conciliates with “wet” biology.

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