Re: [ccp4bb] Inverse 3D profile/threading

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

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Subject: Inverse 3D profile/threading
From: Jason Greenwald jason {- dot -} greenwald {- at -} PHYS {- dot -} CHEM {- dot -} ETHZ {- dot -} CH
Date: 2008-04-02

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Subject: Re: "inclusion body"
From: Mohinder Pal mp11 {- at -} SOTON {- dot -} AC {- dot -} UK
Date: 2008-04-02

Subject: Re: Inverse 3D profile/threading
From: Isaac Westwood isaac {- dot -} westwood {- at -} PHARM {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-04-02

Hi Jason,

While it's not quite what you described, I'd recommend you check out the
Secondary Structure Matching server at the EBI:

http://www.ebi.ac.uk/msd-srv/ssm/ssmstart.html

That will (hopefully!) give you previously deposited structures which share a
similar fold to your query pdb file.

Hope this helps,

Isaac

> I am looking for software or a server to run the 3D-1D profile search
> in reverse: that is I have a new structure (not in yet deposited in
> PDB) and I want to see what sequences might fit well to this 3D
> structure.
> Can someone point me in the right direction?
>
> -jason

CCP4bb navigation

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

Previous message:
Subject: Inverse 3D profile/threading
From: Jason Greenwald jason {- dot -} greenwald {- at -} PHYS {- dot -} CHEM {- dot -} ETHZ {- dot -} CH
Date: 2008-04-02

Next message:
Subject: Re: "inclusion body"
From: Mohinder Pal mp11 {- at -} SOTON {- dot -} AC {- dot -} UK
Date: 2008-04-02