And if you liked SPASM, you'll love the SPASM web-server that Mark Harris has
made:
http://eds.bmc.uu.se/eds/spana.php?spasm
The decapeptide search is similar to the quest for left-handed helices
described in the original publication.
Recipe:
- from the start page, upload a small PDB file that only contains your
decapeptide
- on the parameters page, use:
- large database to search in
- screen on CA atoms only (you're only interested in the backbone
conformation, not the sequence or sidechains)
- finer screening on backbone atoms only
- you can leave the other parameters as they are by default (if you expect
many hits, which slows everything down, you can reduce the RMSD cut-off
initially, e.g. to 0.5 A)
- start the search
- this will typically take 1-5 minutes
- the hits (if any) are presented on the results page and from there you can
quickly explore them, download them or visualise any or all of them with Jmol
--Gerard
On Tue, 15 Dec 2009, MARTYN SYMMONS wrote:
> 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 <[log in to unmask]>
> To: [log in to unmask]
> 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
> [log in to unmask]
>
Best wishes,
--Gerard
******************************************************************
Gerard J. Kleywegt
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:[log in to unmask]
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