Question: Where Can I Get The Secondary Structure Of A Protein?
5
gravatar for Giovanni M Dall'Olio
10.3 years ago by
London, UK
Giovanni M Dall'Olio27k 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 • 5.3k views
ADD COMMENTlink modified 2.3 years ago by Suzanne70 • written 10.3 years ago by Giovanni M Dall'Olio27k
10
gravatar for Suk211
10.2 years ago by
Suk2111.0k
state college
Suk2111.0k 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 10.2 years ago by Suk2111.0k
6
gravatar for Nicojo
10.3 years ago by
Nicojo1.1k
Kyoto, Japan
Nicojo1.1k 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 10.3 years ago by Nicojo1.1k
4
gravatar for Khader Shameer
10.2 years ago by
Manhattan, NY
Khader Shameer18k wrote:

If it is only one sequence you may try PSIPRED server. If you need to work on a large sequence dataset, better to install PSIPRED locally. PSIPRED runs are typically computational intensive.

ADD COMMENTlink written 10.2 years ago by Khader Shameer18k
3
gravatar for Istvan Albert
10.3 years ago by
Istvan Albert ♦♦ 83k
University Park, USA
Istvan Albert ♦♦ 83k 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 10.3 years ago by Istvan Albert ♦♦ 83k
3
gravatar for Darked89
10.2 years ago by
Darked894.2k
Barcelona, Spain
Darked894.2k wrote:

May be a little bit dated, but let me blow my own trumpet (collection of links).

http://openwetware.org/wiki/Wikiomics:Bioinfo_tutorial#Protein_localization_and_structure_prediction

ADD COMMENTlink modified 9 months ago by RamRS27k • written 10.2 years ago by Darked894.2k
3
gravatar for Nir London
10.2 years ago by
Nir London60
Nir London60 wrote:

If you do have the protein structure (PDB file), Stride is also a good option for assigning the secondary structure.

ADD COMMENTlink modified 9 months ago by RamRS27k • written 10.2 years ago by Nir London60
2
gravatar for Kirsley
10.2 years ago by
Kirsley50
Paris
Kirsley50 wrote:

If you want to obtain domains as well as the annotations that come along, you can do it locally with an RPS-BALST. Here for example to obtain Pfam annotations:

rpsblast -i ".$InputPath."/".$item." -d ~/Bioinfo/cdd/Pfam -e 0.000000000001 -o ".$elemt[0]."_Pfam.rpsblast -T T -m 7
  • -i = the input path
  • -d = the database path
  • -e = the e-value cut-off value
  • -o = the output name
  • -T T and -m 7 = to have the output in XML format

You can download all the databases from CDD. You'll obtain external source databases like Pfam, SMART, COG, PRK, TIGRFAM.

ADD COMMENTlink modified 9 months ago by RamRS27k • written 10.2 years ago by Kirsley50
2
gravatar for Thaman
9.5 years ago by
Thaman3.2k
Finland
Thaman3.2k wrote:

You have got all the answers needed for your query. The structure of the protein generally comes after the X-Ray crystallography (which crystallized 80% of the protein structure existed) or NMR technology.

  • Protein Data Bank (PDB) - It's the best and reliable options to find out all the structure available for your protein.

  • Pymol - Visualization and modelling in a 3D. You can visualize either by uploading PDB file or searching through Load structure Plugin.

ADD COMMENTlink modified 9.5 years ago • written 9.5 years ago by Thaman3.2k
1
gravatar for Anuraj Nayarisseri
9.5 years ago by
Indore
Anuraj Nayarisseri750 wrote:

If you want to predict the secondary structure from a protein 3D structure DSSP is one of the best algorithm. following is the link for the same. http://swift.cmbi.ru.nl/gv/dssp/

ADD COMMENTlink written 9.5 years ago by Anuraj Nayarisseri750
0
gravatar for 102316109
4.0 years ago by
1023161090
1023161090 wrote:

How can I download dssp file for large scale of pdb or I can download complete file?

ADD COMMENTlink written 4.0 years ago by 1023161090
0
gravatar for Suzanne
2.3 years ago by
Suzanne70
Dundee, Scotland
Suzanne70 wrote:

Jalview (http://www.jalview.org/) uses the fast and pretty accurate Jpred secondary structure predictor, there is a video on this on YouTube https://youtu.be/z5cVjR9Q3Mw

ADD COMMENTlink written 2.3 years ago by Suzanne70
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