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I have two lists of proteins (including phosphorylated forms). I want to determine which members of each list act on which members of the other list. What online resources exist for finding out what a given protein binds or otherwise interacts with?

I am aware of Uniprot and Phosphosite which have proved useful but I am wondering if there are others that I am not aware of.

Again: the question I am trying to answer is "which proteins from list A interact with proteins from list B and vice-versa?"

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    $\begingroup$ "the question I am trying to answer is 'which proteins from list A interact with proteins from list B and vice-versa?'" You and every biophysicist on the planet. $\endgroup$ – tel Nov 13 '14 at 22:10
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Go to the NAR database site and look for protein domain databases. You have multiple options. Here is the link.

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  • $\begingroup$ This is definitely a good resource. It looks like most of the tools are very specific. I am hoping to find something more general; like string-db.org $\endgroup$ – Slavatron Nov 13 '14 at 18:08
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STRING is one available tool http://string-db.org/ and allowes you to do multiple sequences/names. I would also take an indepth look at what expasy has to offer http://www.expasy.org/proteomics. It is a large collection of bioinformatics tools (far too many for me to go through) and almost always has the tool you want.

(As a side note Expasy also has tools in genomics, structural bioinformatics, and many more, check the left hand tabs on the website for the full list!).

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