Precomputed secondary structure prediction from sequence
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Entering edit mode
7.5 years ago
by0 ▴ 110

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!

pdb secondary 3d beta helix • 2.8k views
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Entering edit mode
4 weeks ago
Jiyao Wang ▴ 170

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". enter image description here

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Entering edit mode
7.5 years ago
User000 ▴ 490

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.

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