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May 7, 2010 10:15 AM Subscribe
Biochemistry filter: Looking for databases about bioactive peptides and their processing. Help me, hive mind!
I'm trying to find a good comprehensive resource for, essentially, processing pathways of bioactive peptides, from preprotein through all known digestion products. I'm specifically interested in endogenous peptides.
Googling turns up lots of resources, but not exactly what I'm looking for. Wondering if the smart folks at MeFi can help me out. Here's what I've found so far:
The Bioactive Peptide Database doesn't look like it's been updated since 2004. It has some info in it--relates preproteins to peptides--but not further digestion/processing.
Uniprot entries of the parent proteins/preproteins will list characterized cleavage products, but there are not separate entries that then list the fate of the product peptides. Kegg Ligand also seems to treat proteolytic processing products the same way, essentially subsumed under the parent protein.
peptideatlas.org is not quite what I'm looking for--it's geared for proteomics analysis.
Though I suspect it's also a proteomics resource, peptidome.org looked promising, but it's in Japanese and I don't speak or read it.
PepBank looks to me like it's geared toward small (<20 aa) synthetic peptides--it doesn't recognize the names of any of the bioactive endogenous peptides I care about.
I'm sort of surprised, what with all the network and pathway building resources available these days, that such a database (or at least the info to draw on to build one!) doesn't already exist. Can anyone help me out? Thanks.
I'm trying to find a good comprehensive resource for, essentially, processing pathways of bioactive peptides, from preprotein through all known digestion products. I'm specifically interested in endogenous peptides.
Googling turns up lots of resources, but not exactly what I'm looking for. Wondering if the smart folks at MeFi can help me out. Here's what I've found so far:
The Bioactive Peptide Database doesn't look like it's been updated since 2004. It has some info in it--relates preproteins to peptides--but not further digestion/processing.
Uniprot entries of the parent proteins/preproteins will list characterized cleavage products, but there are not separate entries that then list the fate of the product peptides. Kegg Ligand also seems to treat proteolytic processing products the same way, essentially subsumed under the parent protein.
peptideatlas.org is not quite what I'm looking for--it's geared for proteomics analysis.
Though I suspect it's also a proteomics resource, peptidome.org looked promising, but it's in Japanese and I don't speak or read it.
PepBank looks to me like it's geared toward small (<20 aa) synthetic peptides--it doesn't recognize the names of any of the bioactive endogenous peptides I care about.
I'm sort of surprised, what with all the network and pathway building resources available these days, that such a database (or at least the info to draw on to build one!) doesn't already exist. Can anyone help me out? Thanks.
Response by poster: I actually adore the biochemical pathways chart! But your suspicion is correct, ideally I'd find something that is query-able in a way that the chart is not. Thanks for the link, though!
posted by Sublimity at 5:54 PM on May 7, 2010
posted by Sublimity at 5:54 PM on May 7, 2010
This thread is closed to new comments.
posted by exogenous at 10:38 AM on May 7, 2010