How to measure the quality of a predicted protein?

Question

[l.souza]

I predicted the tertiary structure of four proteins from their aa sequences using the server Phyre2. How can I measure the quality of the predictions?

Answer 1

[Elisabeth Gasteiger]

Have you tried this?

https://cameo3d.org/ CAMEO continuously evaluate the accuracy and reliability of predictions

Answer 2

[Joe]

There are many metrics you could use to examine the quality.

1. Measure the RMSD to a known homolog (ie. what the Phyre2 server used as a threading template. If there are any regions of high RMSD that would suggest they aren't super likely.

2. Measure dihedral angles for the protein chain for a Ramachandran plot, if you have any outliers, it suggests your simulation has an implausible bond angle for the backbone.

There are loads of webservers for this kind of thing, so I'd start by just googling a few to see what you can find.

Few examples: http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/index.html http://zhanglab.ccmb.med.umich.edu/I-TASSER/