Re: [ccp4bb] protein-protein docking programs

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From: Raji Edayathumangalam redayath {- at -} MAIL {- dot -} ROCKEFELLER {- dot -} EDU
Date: 2008-05-02

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From: Gerard DVD Kleywegt gerard {- at -} XRAY {- dot -} BMC {- dot -} UU {- dot -} SE
Date: 2008-05-02

Subject: Re: protein-protein docking programs
From: Ronan Keegan r {- dot -} m {- dot -} keegan {- at -} DL {- dot -} AC {- dot -} UK
Date: 2008-05-02

Hi Jerry,

I've not got a whole lot of experience with docking programs but I have
used 3D-dock (http://www.sbg.bio.ic.ac.uk/docking/) to do docking trials
between two proteins and found it to be easy to set up and use. It uses
an algorithm that mainly looks at surface complimentarity between the
two proteins but it helps a lot if you use some biological information
to restrain the results.

Hope this helps,

Ronan

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 <-- 2008 <-- May 2008 <-- 02 May 2008

Previous message:
Subject: Re: sa omit map
From: Raji Edayathumangalam redayath {- at -} MAIL {- dot -} ROCKEFELLER {- dot -} EDU
Date: 2008-05-02

Next message:
Subject: Re: sa omit map
From: Gerard DVD Kleywegt gerard {- at -} XRAY {- dot -} BMC {- dot -} UU {- dot -} SE
Date: 2008-05-02