[Dock-fans] Fwd: virtual screening using dock?

CAI Qixu caiqixu at gmail.com
Fri Jun 26 09:36:06 PDT 2009


Qixu Cai
Email: caiqixu at gmail.com
Xiamen University, Fujian, China


---------- Forwarded message ----------
From: CAI Qixu <caiqixu at gmail.com>
Date: 2009/6/27
Subject: Re: [Dock-fans] virtual screening using dock?
To: venkat <vkabas at yahoo.com>


Hi,
Do you know how these two proteins interact? If you know, I think you can
form a new pdb file with these protein pdb which interact. And you can use
the new pdb for docking.

Qixu Cai
Email: caiqixu at gmail.com
Xiamen University, Fujian, China


2009/6/25 venkat <vkabas at yahoo.com>


> Hi
>
> I am trying to find the small molecule that could interfere with protein -
> protein interface. I am new to docking and have few questions in mind before
> I start ,
>
> I know for the protein without complex can be used for docking as whole.
>
> For protein - protein interactions, I do have to keep both complex as
> receptor molecule and search for small molecule that binds near the
> interface?That did not make sense cause small molecule is not going to
> interfere with the already filled interface with other protein.
>
> I think I could use two pdbs separtely and trying to find the small
> molecule to the known interface region?
>
> any help could be appreciate
>
> thanks
> venkat
>
>
>
>
>
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