I have 6 receptors and only 1 ligand. In the meantime I interested to do the docking in all these receptor. Is there any way where we have a generalised way to dock this compound to these receptor so that I can save my time.
Hi,
You can use autodock vina though you will have to use consider each receptor one at a time but the procedure in vina is completed very fast so it will save your time.
But the question here is are you trying to find a potential drug target for a particular ligand if yes then you should try reverse docking approach. Hope this helps
Regards
but danish can we do like.....usually we make some library of compounds and then does the docking for a particular receptor. Can we make it inverse as to make a library of receptor and fixed the docking of a particular ligand at the site of already embedded ligand in those receptors. Can we do that??
Hi,
6 receptors is not exactly the typical task for an automated docking procedures. In my opinion this can be more efficently and reliably performed by docking molecules to each receptor one at time. For higher number of targets you may have a look to:
http://www.ncbi.nlm.nih.gov/pubmed/11276090
cheers
Yes as i have mentioned above that you can use reverse docking approach to find a potential target for your ligand.
ya I agree Danish and stefano. But tell me if I have more than 200 receptors than what will I do?
Then surely it will be not feasible by doing one by one as it will take long time.
Then ill suggest you to use servers like TarFisDock which perform reverse docking or you can try pharmapper a web server for potential drug target identification using pharmacophore mapping approach.
Hai Aravind, If you have the access to the Schrodinger software suite, Then you can use the Virtual Screening workflow option where you can automatically prepare the set of any number of receptors and then automate the docking process, but if you don't have the access to it. Then you can use the Inverse docking approach as well.
There seem to be different purposes for docking a single ligand to multiple receptors. As Stefano said, 6 is a very small number and will take a very short time to do individually with better thoroughness.
If you are trying to identify a receptor for the ligand- then 'reverse docking' is the way to do it (TarFisDock and PharmMaper, as suggested by Danish, have also been recommended elsewhere). If you do not have access to an expensive software suite like Schrodinger, and want to target a very specific set of receptors that isn't available as an option with a current server, I would suggest you write a batch file to run 'autodock vina' in an automated mode. With a very large number of receptors, you will want to apply a common grid box that will work for all receptors- so it will have to be all encompassing.
Good luck!
PS. idTarget (see link below) allows you to specify a list of receptors for docking your ligand of interest.
http://idtarget.rcas.sinica.edu.tw/step.php
Coming directly to the point - the closest you will get interms of method is something called Multiple Copy Simultaneous Search (MCSS).
It is a Molecular dynamics technique where you create multiple copies (Replicas) of a ligand in an around the binding site. The replicas don't see each other. Each of them converge to their own minimums and you then look at clusters and identify sites.
Your case can work with this method well. However I will recommend revising your strategy of saving time - your results need to be statistically significant - in simulations/docking studies - statistics matter.
Hope this helps.
Good Luck.
Best,
/A
6 receptors IS exactly the typical task for MY automated docking procedure. If you have a Schrodinger license you can (must) use my automated ensemble docking pipeline:
https://github.com/dcorrada/RICEDDARIO/wiki/DONKEY
BTW, I dislike the default virtual screening proposed by Schrodinger. I mean, Knime is a suitable tool to accomplish such tasks, but their internal job manager is really awful if someone plans to perform parallel jobs. For this reason I have created a personal pipeline in which Schrodinger jobs are launched and monitored by my queue manager.
For 200 receptor DONKEY runs as well. It not depends by the script, but your computational resources...
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