Question: Supersecondary Structure Prediction
3
gravatar for Jamand
8.6 years ago by
Jamand110
European Union
Jamand110 wrote:

Dear All,

Do you know any tool to predict supersecondary structure in proteins?

thank in advance.

prediction protein structure • 3.0k views
ADD COMMENTlink modified 8.6 years ago by Anuraj Nayarisseri740 • written 8.6 years ago by Jamand110

What is your data type ? Sequence or Structure ? Are you looking at any specific type of supersecondary structure ?

ADD REPLYlink written 8.6 years ago by Khader Shameer18k
3
gravatar for Jarretinha
8.6 years ago by
Jarretinha3.3k
São Paulo, Brazil
Jarretinha3.3k wrote:

You can use Threader and its derivates. It can statistically recognize the fold of your protein/domain. It's pretty slow, but quite reliable.

ADD COMMENTlink written 8.6 years ago by Jarretinha3.3k

fold != supersecondary structure. To the best of my knowledge THREADER is a fold recognition program, not a supersecondary structure prediction program.

ADD REPLYlink written 8.6 years ago by Khader Shameer18k

That's true. Nevertheless, you can use it for SSS prediction if you don't have a target in mind (e. g. transmembrane helices). You just need to divide your sequence in appropriate pieces. It's quite brute force, it's slow but works. Test it yourself using some known pi-helices. Besides this approach, I don't know a generic SSS server/program.

ADD REPLYlink written 8.6 years ago by Jarretinha3.3k
3
gravatar for Khader Shameer
8.6 years ago by
Manhattan, NY
Khader Shameer18k wrote:

Not sure if there is a consensus prediction program which can predict various supersecondary structures (for example Helix-Turn-Helix, Beta-hairpins etc.) from sequence or structure information. Structure prediction is an area of active area research and various algorithms are available. I would recommend you to make a list of your supersecondary structures of interest and then search for servers/program which could predict such features from sequence information.

For example:

Helix-Turn-Helix prediction: http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_hth.html Beta-hair pin prediction: http://www.imtech.res.in/raghava/bhairpred/supli.html

Also refer to Chou K. C's publications and various secondary structure prediction servers from G. P. S. Raghava's group for a good background reading on available supersecondary structure prediction algorithms.

ADD COMMENTlink modified 8.6 years ago • written 8.6 years ago by Khader Shameer18k

Khader, your links proved much more useful than I thought initially! I've caught myself using Raghava's servers regularly by now (and recommending).

ADD REPLYlink written 8.5 years ago by Jarretinha3.3k
1
gravatar for Suk211
8.6 years ago by
Suk2111.0k
state college
Suk2111.0k wrote:

If you have the PDB file for your protein of interest, you can use promotif to calculate the super secondary structures.

ADD COMMENTlink written 8.6 years ago by Suk2111.0k
1
gravatar for Anuraj Nayarisseri
8.5 years ago by
Indore
Anuraj Nayarisseri740 wrote:

try out the following tools

http://myhits.isb-sib.ch/cgi-bin/motif_scan

http://www.ebi.ac.uk/Tools/pfa/iprscan/

these are the best tools

ADD COMMENTlink written 8.5 years ago by Anuraj Nayarisseri740

Anuraj: MotifScan and iprscan is for functional motif prediction. jamAnd is looking for supersecondary structure information, not functional motifs/patterns.

ADD REPLYlink written 8.5 years ago by Khader Shameer18k
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