membrane bound proteins

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ann bijnens
ann bijnens's picture
membrane bound proteins

Hi,

Does anyone know a convenient way to identify membrane bound genes given a list of hundreds of genes?

AP

Richard Taylor
Richard Taylor's picture
You won't find any region of

You won't find any region of similarity between all membrane bound proteins, but there are similarities between groups. Look up Pleckstrin homology for example - proteins sharing a similar mechanism of binding lipid anchors:
http://www.jbc.org/cgi/content/full/275/20/14873

Are you differenciating between membrane bound and transmembrane? Transmembrane proteins are easier to identify from sequence.

The answer to your question could involve literature mining - what are you starting from - is your list a list of names, sequences, fragments of sequences...?

bgood
bgood's picture
There are a number of tools

There are a number of tools for predicting protein subcellular localization out there that can help. Many of these are linked to from here

http://www.psort.org/

ryan_m
ryan_m's picture
bgood wrote:There are a

bgood wrote:

There are a number of tools for predicting protein subcellular localization out there that can help. Many of these are linked to from here

http://www.psort.org/

Yes, psort would be a good solution for eubacteria, though the eukaryota version is quite old. I'm actually unclear at the moment whether you want to find "known" membrane-localised proteins or predict localization (which is what psort and others do). One is a text-mining problem while the other is a classification problem. If you want to predict localization based on signal peptides in the protein sequence, try signalP or SubLoc.
As for text-mining the known ones, I can't help you there.
Cheers.
Ryan

bgood
bgood's picture
Interesting that you should

Interesting that you should try to seperate text-mining from classification. PSORT-b's main competition comes from a program called Proteome Analyst that builds its classifier by integrating Blast and and text/tag based classifiers. Pretty cool really.

http://www.cs.ualberta.ca/%7Ebioinfo/PA/Sub/index.html

There are links to lots of different predictors up on the PSORT website - I don't think their (PSORTs) new eukaryotic predictor is ready , but many of the others are.

sichan
sichan's picture
I found that TMpred is a

I found that TMpred is a simple tool to use, but there are no doubt other ones out there.

You might want to check out this paper to see the tool in use:

Example of TMpred in use

sichan
sichan's picture
Another transmembrane

Another transmembrane prediction tool developed by researchers at Harvard Medical School:

PLoS ONE Paper