Re: [ccp4bb] protein-protein docking programs

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: COOT ramachandran plot
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-05-06

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From: Andreas_Förster docandreas {- at -} GMAIL {- dot -} COM
Date: 2008-05-07

Subject: Re: protein-protein docking programs
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2008-05-07

On May 6, 2008, at 18:57, Jerry McCully wrote:

> Hi, All:
>
> Thanks a lot for the prompt reply from all of you.
>
> Probably I have another problem.
>
> My complex was mediated by two separated interfaces between
> the receptor and two subunits of the ligand.
>
> I tried HEX and the ClusPro server to dock the homologous
> ligand. however, the docking results were focused on one subunit.
>
>
> How can I restrict the docking around these two interfaces?

(Oh, well, I guess that now I will have to repeat my previous answer
in private, in public since it is now made public anyway.)

Try HADDOCK.

A.

>
>
> Or I just superimpose the ligands and do some local
> minimization to get kind of detailed binding model of the receptor.
>
> Thanks a lot again,
>
> Jerry
>
> From: a.perrakis@nki.nl
> To: for-crystallizaiton@HOTMAIL.COM
> Subject: Re: [ccp4bb] protein-protein docking programs
> Date: Fri, 2 May 2008 18:11:57 +0200
>
> Try HADDOCK.
>
> I think the way to use it will be obvious when you read the doc/
> papers, but do not hesitate to ask me if I can help more.
> I think its kind of ideal for your case.
>
> A.
>
> On May 2, 2008, at 17:18, Jerry McCully wrote:
> Hi, All:
>
> Recently we solved a complex structure between two proteins,
> which indicated the interaction was kind of
> rigid.
>
> Therefore we want to test the binding mode of the receptor with
> another homologous ligand(very similar structure, RMSD 2.4 angstrom).
>
> Can somebody recommend a sophisticated docking program to do this?
>
> Thanks a lot.
>
> Jerry McCully
>
>
>
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>
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CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: COOT ramachandran plot
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-05-06

Next message:
Subject: scala on mac osx - off topic, really
From: Andreas_Förster docandreas {- at -} GMAIL {- dot -} COM
Date: 2008-05-07