Any database that shows protein-protein interactions??

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cooldogkey
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Any database that shows protein-protein interactions??

Postby cooldogkey » Wed Jul 13, 2011 2:58 pm

I have a quick question for you all
Do you know any database that shows protein-protein interactions in yeasts?
I am trying to find a group of transcription regulators that act as complexes..

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Doug
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Postby Doug » Wed Jul 13, 2011 6:00 pm

There are two tools I have used to visualize protein-protein interactions that could be helpful to you. My favorite is Cytoscape. You can import interaction data sets and visualize them. The visualization is incredibly customizable. It also allows you to pretty easily load your data sets on top of these known interactions. And there are plugins that let you do some further analysis as well. There is a pretty steep learning curve with this one. And there are often compatibily issues with plugins that dont work with the current version. But overall, i highly recommend it.

STRING is much easier to use and allows you to perform the basic stuff that cytoscape does but without the bells and whistles. But it is user friendly and a good place to start.

I have never used it but BioGRID is another place to look.

Craig
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Postby Craig » Wed Jul 13, 2011 6:14 pm

I don't know much about this topic, but I have seen that UniProt has data about protein–protein binary interactions. It seems to be getting the information from IntAct.

Artur
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Postby Artur » Wed Sep 21, 2011 5:56 am

It should be useful : http://www.pathguide.org/

woa
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Postby woa » Sun Oct 16, 2011 7:58 am

For an extensive list of databases check this site:
http://www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml
To retrieve data using appropriate queries click the MIQL syntax reference at the right of the page
The OSPREY network visualization software can download the yeast(for some other organism too) interaction data from Biogrid.
But it can be a bit dated.
http://biodata.mshri.on.ca/osprey/servlet/Index

sosborne
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Postby sosborne » Mon Jun 22, 2015 10:13 am

I know this is an old thread I'm adding to but just in case anyone drops by ....


Proteomics Resources including Databases, Tools and Visualisation software

Please note that there is pretty comprehensive list of >250 links to Proteomics Resources including Databases, Tools and Visualisation software at Pastel BioScience's website ...
http://www.pastelbioscience.co.uk/re...databases.html

also take a look at the list of conferences, symposiums, workshops and seminars at ...
http://www.pastelbioscience.co.uk/re...nferences.html

these are updated regularly but we would appreciate any updates, additions or comments.

Hope you find these resources useful


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