Precomputed secondary structure prediction from sequence

Question

[by0]

Hi,

Most services that predict secondary structure from sequence, such as psipred, have an online webserver or a program you'd have to run locally (which would take quite a bit for a whole proteome).

e.g. http://bioinf.cs.ucl.ac.uk/psipred/result/0fc9a438-c3d8-11e3-a745-00163e110593

I was wondering if anyone knew a reseource that had precomputed secondary structure predictions I can download for my proteome of choice (Yeast).

I would assume at least of one the services would run it (for example) on all of uniprot and provide the predictions in a database or flatfile.

Thanks in advance!

Answer 1

[Jiyao Wang]

Since the AlphaFold protein database provides predicted structures for many UniProt proteins, you can try the following with iCn3D. First, open a UniProt ID with the menu "File > Retrieve by ID > AlphaFold UniProt ID", e.g., https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?afid=A0A061AD48. Then open the detailed sequence view "Analysis > Seq. & Annotations : Details" to see the secondary structures. This whole process can be written in a Node.js script to run in command line. Some examples are at https://github.com/ncbi/icn3d/tree/master/icn3dnode.

Interactively, you can click "Helix Sets" and "Sheet Sets" button in the sequence window to generate sets. Finally export the sets in a text file with the menu "File > Save Files > Selection File".

Answer 2

[User000]

I think one of the best solutions is to write a (Python) script yourself. SVM and PSIPRED prediction methods show higher Q3, you can base on algorithms of one of these two. Run PSI-BLAST of your fasta files against your DB to extract sequence profiles, then generate scoring matrices, do cross-validation and statistical validaton.