Question: Protein Functional Classes
gravatar for Vladimir Chupakhin
8.4 years ago by
Toledo, Spain
Vladimir Chupakhin520 wrote:

Can you, please, suggest me the protein functional classes according to scenario: Class should have in the one specific function - for example metabolizing and binding specific compound class. For example, participate in steroid pathway. EC number works, but does not include a lot of other targets of non-enzyme nature.

function database protein • 5.0k views
ADD COMMENTlink modified 5.5 years ago by Biostar ♦♦ 20 • written 8.4 years ago by Vladimir Chupakhin520

Besides GO, the standard classification databases are maybe your best shot: NCBI CDD and InterPro.

ADD REPLYlink written 8.4 years ago by Michael Schubert6.9k

I agree InterPro seems reasonable, it's probably better than GO (more specific).

ADD REPLYlink written 8.3 years ago by boczniak767680
gravatar for Sean Davis
8.4 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

You might have a look at the Gene Ontology. If you have a specific source for your protein data (UniProt, for example), you may find that there are cross-references between your proteins and the Gene Ontology allowing you to functionally categorize the proteins according to Gene Ontology categories.

ADD COMMENTlink written 8.4 years ago by Sean Davis26k

I do have uniprot for all of the entries, but GO require a lot of work to do. I was thinking about maybe more simple and easy solution.

ADD REPLYlink written 8.4 years ago by Vladimir Chupakhin520

Download human GO annotations (or whatever organism you like) from here for example. Then, find the GO terms of interest on the GO website.

ADD REPLYlink written 8.4 years ago by Sean Davis26k
gravatar for Khader Shameer
8.0 years ago by
Manhattan, NY
Khader Shameer18k wrote:

Along with GO you may also check Protein Feature Ontology or protein annotation databases like Panther Classification System specifically designed using protein class level annotations.

You can also utilize protein domains or clan based classification in Pfam. If you have structural data you may also consult classification in the level of protein families, super families or folds (See SCOP/CATH).

ADD COMMENTlink written 8.0 years ago by Khader Shameer18k

thank's Panther should work for me

ADD REPLYlink written 8.0 years ago by Vladimir Chupakhin520
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