Is There A Database Or Service That Connects Aminoacid Sequences To Fold Motifs

Question

[Raygozak]

Hi, does anyone know about a database that relates sequences of aminoacids to motifs of folds?

By this I mean maybe the last fifteen aminoacids of a protein have been observed to fold in a somewhat conserved way. I'm not looking for the entire protein fold but subsequences that might match a known common motif of folds. I have already tried several databases. The one that is closer is the Protein Folding database but it doesn't work well

http://pfd.med.monash.edu/public_html/index.php?module=dsm&page=searchresults&title=Advanced%20Search%20Results

Thanks

[Alex Reynolds]

Perhaps you could search for Pfam families that match closely to your subsequence?

[sarahhunter]

Could you be a bit more specific about what you mean by a fold? InterPro relates the classifications produced by SCOP and CATH (and their partner databases SUPERFAMILY and GENE3D) to sequence; the Genome3D project might be of similar use.

Answer 1

[Giovanni M Dall'Olio]

You can try:

• The "Conserved Domains" database at NCBI. Maybe you didn't notice, but when you do a Blast search using NCBI-Blast, the page automatically returns you a representation of the conserved domains. This is the database from which these predictions are from.

• Prosite from Expasy is probably the most popular choice. Prosite represents protein domains as patterns or matrices - for example, a domain can be represented as a regular expression like A-T-H-[D or E].

• PFAM uses another method to identify sequences, based on Hidden Markov Models (see also HMMER for a more detailed description of the method). It should be more accurate than prosite, but also identify less matches.