Question: What kind of information is good to know about a protein (or domain) and where can we find it?
1
gravatar for mparadis92
4.4 years ago by
mparadis9240
Canada
mparadis9240 wrote:

Hello. This is kind of a weird question and I'm going to try to make it easier to understand. I'm a student in bioinformatics for only 2 years now so go easy on me :)

Long story short, I predicted disorder scores for every amino acids in every protein from ~50 phages (about 3000 proteins) using DISOPRED3. Only a few had domains of about 30 disordered residues. I want to get the most information about the protein closest to the consensus of an alignment I did with all those highly disordered proteins.

I'm a good programmer but I lack skills and knowledge when it's time to "talk" about a protein or a domain. I know I can use PDB or other databases but why? To find a protein with a similar domain and get information about it's function? What is the typical process to gather useful information about proteins?

Thanks a lot to whoever takes the time to help me understand the way to do this the right way! 

ADD COMMENTlink modified 4.4 years ago by candyton990 • written 4.4 years ago by mparadis9240

It depends on what you want to know about the protein which in turn depends on the question you're interested in. What do you want to know/achieve by predicting disordered domains ? What's the question/hypothesis behind your work ?

This being said, information about proteins is scattered in different databases with each usually focusing on a particular type on information. However a good starting point would be Uniprot which organizes and centralizes all types of protein annotation.

ADD REPLYlink written 4.4 years ago by Jean-Karim Heriche21k
0
gravatar for candyton99
4.4 years ago by
candyton990
United States
candyton990 wrote:

Usually, we'd use a tool to help analyse the protein. And I think that's what most researchers do while trying to gather information,PRECIS, for instance. 

 

ADD COMMENTlink written 4.4 years ago by candyton990
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