[gmx-users] setting constraints to incomplete protein structures

[wk yeo]

Hello,

Usually, the protein-ligand complexes which we download from the PDB contain ligands which I am not interested in. But I have other ligands which I think might be able to dock into the same binding pocket. Of course, it is a 'simple' matter of docking these 'new' ligands into the holo protein structure (obtained by deleting the original ligand). But I would like to think that most of the proteins obtained this way are only in conformations which are favourable for the original ligands. Therefore, I am guessing that conducting some short MD runs will allow the binding pocket to 'adapt' properly to the newly docked ligands and/or vice versa. At the moment, I have not been able to conduct the MD runs due to the problems discussed in my previous postings. But I foresee that I will have a dilemma over which conformation from the entire MD to use. Do I take the average (mean) conformation? Or do I take the last (final) conformation? The solutions will have to be found in the future once I get my MD running.

regards,
wk yeo

________________________________

Date: Tue, 7 Oct 2008 11:36:57 +0530
From: viveksharma.iitb at gmail.com
To: jalemkul at vt.edu; gmx-users at gromacs.org
Subject: Re: [gmx-users] setting constraints to incomplete protein structures
CC:


Hi yeo,
I have one query related to the MD you are trying.
 What I understood here is you are trying different conformation of your protein molecule for docking it with ligand (please, correct me if I am wrong)
I am also trying the same, But not finding any criteria to pick up the conformation of protein to try it further for docking ?
Do you have any insight into the same ?

With Thanks,
Vivek
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