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PostPosted: Thu May 03, 2012 4:31 pm 
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I am using 2 different means to identify the docking site within a comparative/homology protein model. They are....
1) Supperimpose the X-ray model (which was used as a template) onto the newly modelled protein and allign the gridbox over the ligand/binding site of the X-ray structure and...
2) Identify protein pockets with CASTp (Still trying to figure out which predicted pocket is most accurate -biggest/smallest/scoring? Help here too pls!)

I want to find out, which of these 2 techniques are more accepted and more accurate and if there are any other techniques which can accurately predict the binding site?

Any help would be greatly appreciated!

Thank you!


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PostPosted: Thu May 03, 2012 9:42 pm 
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Hi,

you could have a look at AutoLigand, that is a binding site predictor based on the AutoGrid maps. It has been tested successfully on a number of protein targets[1], and it helped identifying a novel exo-site on HIV protease [2].

Hope it helps,


Stefano



[1] http://onlinelibrary.wiley.com/doi/10.1 ... 21645/full
[2] http://onlinelibrary.wiley.com/doi/10.1 ... 0943.x/pdf


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PostPosted: Wed May 23, 2012 7:21 am 
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Thank you! This was extremely useful!


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