Re: [ccp4bb] 3D search for peptide conformers?

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

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Subject: Re: H32 or R 3 2 :H
From: Martyn Winn martyn {- dot -} winn {- at -} STFC {- dot -} AC {- dot -} UK
Date: 2009-12-15

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Subject: Re: H32 or R 3 2 :H
From: "George M {- dot -} Sheldrick" gsheldr {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2009-12-15

Subject: Re: 3D search for peptide conformers?
From: MARTYN SYMMONS martainn_oshiomains {- at -} BTINTERNET {- dot -} COM
Date: 2009-12-15

I think SPASM by Gerard Kleywegt is a great tool for this sort of thing - you can set the similarity matrix threshold to make it more or less sequence independent (it still calculates the sequence match which is good for looking for key residues in the motif like structurally required GLYs). You can also restrict it to just CA positions. And you can set the thresholds for the search to narrow down on the basis of rmsd.

J Mol Biol. 1999 Jan 29;285(4):1887-97.
Recognition of spatial motifs in protein structures.
Kleywegt GJ.

You can download the program and a search library - currently july 2008 pdb I think (culled to 99% seq ident. is the best one). But could be something more recent available?

Good luck
Martyn

Martyn Symmons - Cambridge
________________________________
From: Patrick Loll
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, 14 December, 2009 20:02:53
Subject: [ccp4bb] 3D search for peptide conformers?

I have a 10-residue stretch of a protein that adopts an interesting conformation; I'd like to know if this conformation occurs in other proteins. I'd welcome suggestions for tools that will allow me to to search for this peptide conformation in the PDB.

I naturally thought of DALI, but it seems to require a minimum length of 30 residues.

Thanks,

Pat

---------------------------------------------------------------------------------------
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 19102-1192 USA

(215) 762-7706
pat.loll@drexelmed.edu

CCP4bb navigation

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

Previous message:
Subject: Re: H32 or R 3 2 :H
From: Martyn Winn martyn {- dot -} winn {- at -} STFC {- dot -} AC {- dot -} UK
Date: 2009-12-15

Next message:
Subject: Re: H32 or R 3 2 :H
From: "George M {- dot -} Sheldrick" gsheldr {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2009-12-15