Hi to all,
I'm approaching to the haddock web-tool for the first time. I got the username and password for the easy interface.
I'd like to know wheather i'm on the right way.
Once I've uploaded the pdb files to be docked, I have to specify both the active and the passive residues.
In order to determine the active residues I have performed an NMR titration of the unlabelled protein with the labelled ligand and vice versa. Then I've calculated the chemical shift perturbation.
Now I have to determine which among them are the active residues in the protein-ligand interaction.
So, shall I have to submit the pdb to a SASA (solvent accessible surface area) calculation program and chose the chemical shift perturbation residues that match with those solvent accessible by the SASA program?
is it correct?
do you advise any software/webtool? (i know NACCESS, but there is a very tedious procedure that i have to follow in order to get codes for decrypt the rar files)
thank you.
what have i do for the passive residues, is reliable the option on haddock that allows to determine them automatically?
Bye
Hi Antonio,
Your active-residue-case has been explained over here: https://www.wenmr.eu/wenmr/case-study-preparing-input-files-manual-haddock-run
Regarding the passive residue definition: You only need to turn on the "Define passive residues automatically around the active residues" option of the server.
Hope this helps,
Cheers
Ezgi
Hi, I have recently published two papers in which haddock was used for docking. In the experimental part of it you can find the methodology to determine the active residues (passive are automatically determined):
http://pubs.rsc.org/en/content/articlelanding/2013/ra/c3ra45933k/unauth#!divAbstract
http://pubs.acs.org/doi/abs/10.1021/ml4002908
If you have some questions do not hesitate to contact me.
Sincerely
simone
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