Question: Where Can I Get The Secondary Structure Of A Protein?
2
gravatar for Giovanni M Dall'Olio
10.7 years ago by
Barcelona, Spain
Giovanni M Dall'Olio420 wrote:

As in the title... I have a protein and I would like to know its secundary structure. I couldn't find it in uniprot, althought I tought they had annotations for it there. In the end I have used a predictor (jpred) but there it should be a database somewhere.

sequence protein structure • 1.3k views
ADD COMMENTlink modified 10.6 years ago by User 82260 • written 10.7 years ago by Giovanni M Dall'Olio420
4
gravatar for Suk211
10.7 years ago by
Suk21160
state college
Suk21160 wrote:

If you have the PDB file then you can use the standard tool called DSSP , it is supposed to be the gold standard for obtaining secondary structure. In case you just have sequence then I personally prefer PSIPRED , it takes evolutionary information into account to predict the secondary structure . According to CASP evaluation it is one of the best secondary structure predictor available.

ADD COMMENTlink written 10.7 years ago by Suk21160
3
gravatar for Nicojo
10.7 years ago by
Nicojo40
Nicojo40 wrote:

I think you found the best answer yourself: use a predictor! There are several out there...

You suggest that there should be a Secondary Structure Database. I'm not sure that makes much sense, let me explain my point of view (which may not be that of everyone): most often, the data that is found in databases is the "state of knowledge" of the described object, based on experimentation.

That may be the case for secondary structures of proteins, but only in the case where the said proteins have been crystalized. In those cases, it is not only the secondary structures but also the tertiary structures (with the caveat that the crystal structure of a protein does not prove "all" states that a protein may take in real "dynamic" physiological conditions).

For all those proteins that have not been crystalized, then we can only rely on predictions. And I use them quite frequently: they are extremely useful! But as far as I know, no prediction is accepted as fact. They're "educated guesses" that are often correct, but sometimes wrong. The results may differ from one prediction method to another. Also they change each time the algorithms are improved...

If there was a database of predicted secondary structures, people would likely take them for granted (make the equation prediction = fact) which would be quite "unscientific".

I think such a resource would be more of a hindrance than an asset to the scientific community...

ADD COMMENTlink written 10.7 years ago by Nicojo40
1
gravatar for István Albert
10.7 years ago by
István Albert ♦♦ 310
University Park
István Albert ♦♦ 310 wrote:

Protein structure prediction is a complex issue that is likely to require multiple approaches. There are many methods/tools listed at the

ADD COMMENTlink written 10.7 years ago by István Albert ♦♦ 310
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