secondary structure database search

Przemko przemko at reks.uia.ac.be
Mon May 29 03:43:39 EST 1995

>Chris Sanders' group has set up the PredictProtein server; try
>phd at embl-heidelberg.de
>with a 'help' in the message.
> R.Doelz         Klingelbergstr.70| Tel. x41 61 267 2247  Fax x41 61 267 2078|
> Biocomputing        CH 4056 Basel| electronic Mail    doelz at ubaclu.unibas.ch|
> Biozentrum der Universitaet Basel|-------------- Switzerland ---------------|
><a href=http://beta.embnet.unibas.ch/>EMBnet 
Switzerland:info at ch.embnet.org</a>

This server will do the prediction of the secondary structure (I tried to use 
it in the past with a reasonable success which would be greater if the outpu 
weas graphical...) but it is not possible to search a database. Sometimes the 
server would return another homolog from SwissProt but ONLY if it was really 
basically identical. What I am asking for is a search where I get as an output 
a list (like in BLAST or even better in FASTA) of possibly related proteins 
(from the point of view of secondary structures). In other words, if I have on 
my protein three beta-sheets followed by a helix of a given lenght and then a 
sheet again, Iw ould like to know what other proteins in database have similar 
order/size/distribution of those secondary structures.

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