What Is The Status-Quo In Secondary Structure Prediction ?
Entering edit mode
11.7 years ago
Giselle ▴ 130

Hi there,

i heard from a friend of mine, that 3d structure prediction is not accurate enough to use it as a tool for research.

On the other hand secondary structure prediction is pretty accurate .

  1. Why is there such a big discrepancy ?
  2. How accurate are those methods in percent ?
  3. I want to use a secondary structure predictor and compare 2 ortholog genes. How would you do it ? What important information can i get from secondary structure prediction ? ( besides alpha and beta chains )

my background : microbiology undergrad ; writing my thesis ; soorry for my bad english

secondary prediction tool • 2.7k views
Entering edit mode
11.7 years ago
Lyco ★ 2.3k

The accurace of secondary structure prediction depends on the method (obviously), but also on the target protein and on the definition of what you call a 'correct prediction'. It is probably around 70-80% correct on a per-residue basis. Maybe others can give you better numbers.

I must caution against 'comparing the 2ndary structure prediction of orthologs'. First, if they are orthologs, chances are good that the secondary structure will be identical. If there are (subtle) differences, they will most likely no be picked up by the prediction methods. It is important to know that the best prediction servers (Predictprotein, PSI-pred, Jpred) do not use a single sequence for the prediction but rather an alignment of related sequences (including orthologs). This is because the conservation properties contain important information that improve structure prediction. For some methods you can (or even have to) provide an alignment directly, while for other methods you submit a single sequence but the programs will then start to search for homologs (and align them) on their own. As a consequence, you cannot expect to see different predictions for related sequences.

Some explanation on the purpose and pitfalls of secondary structure prediction can be read in the manual of Predict Protein in these paragraphs. Programs/servers that you might want to check include PredictProtein, Psipred and jpred.

Tertiary structure prediction ab initio is not ready for prime time,although it is actively being worked on and makes some progress. The reason for this discrepancy is that the problem is much harder (many more parameters to predict) than a pure 2ndary structure prediction. However, a 3D structure prediction is absolutely feasible if you have a good template with known 3D structure, which is related to your protein of interest. Again, by this method you will never be able to see differences between orthologs. If you really want to see subtle differences you have to go for the real structure.

Entering edit mode
11.7 years ago
Shigeta ▴ 460

just wanted to add response to (3). there are also predictors for beta turns, 310 helices, beta bulges, transmembrane helices and disordered regions as well. (See DSSP for a good list of secondary structure types http://en.wikipedia.org/wiki/DSSP_(protein) )

Looking at ss predictions for families of closely related proteins can be helpful I say. Try laying them over your family alignment - its really useful.


Login before adding your answer.

Traffic: 1818 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6