Protein sequence features from sequence inputs?

Question

[Bioaln]

Hello!

I am currently dealing with some sequence processing and I came to the following problem. I have a bunch of fasta sequences , representing my proteins. How do I find important structural features in such data? I realize this can be done almost exclusively with some database of annotated features, is there any of such kind?

So for example I want to know, how many there are alpha helices, beta strands and so on for each fasta sequence.

Thanks!

Answer 1

[natasha.sernova]

See sites like these ones:

https://www.predictprotein.org/

http://molbiol-tools.ca/Motifs.htm

http://molbiol-tools.ca/Protein_secondary_structure.htm

Answer 2

[cdsouthan]

Use the InterPro engine as the most informative first pass. 2nd struc prediction not that useful, but gene3D inside InterPro will tell you structure matches with known 2nd struc

[Bioaln]

Thanks for the suggestion!