Re: [ccp4bb] protein-protein docking programs

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CCP4bb <-- 2008 <-- May 2008 <-- 06 May 2008

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Subject: Re: Negative density around C of COO-
From: "Nave, C (Colin)" colin {- dot -} nave {- at -} DIAMOND {- dot -} AC {- dot -} UK
Date: 2008-05-06

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Subject: Re: Refmac
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-05-06

Subject: Re: protein-protein docking programs
From: Jerry McCully for-crystallizaiton {- at -} HOTMAIL {- dot -} COM
Date: 2008-05-06

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?

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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CCP4bb navigation

CCP4bb <-- 2008 <-- May 2008 <-- 06 May 2008

Previous message:
Subject: Re: Negative density around C of COO-
From: "Nave, C (Colin)" colin {- dot -} nave {- at -} DIAMOND {- dot -} AC {- dot -} UK
Date: 2008-05-06

Next message:
Subject: Re: Refmac
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-05-06