Description - Protein Secondary Structure Prediction

Description
Protein Secondary Structure Prediction
from the sequence

Method :

The joint prediction method for protein secondary structure combines the result of five different prediction methods. In the original New Joint Method, the five methods are: QS: Qian-Sejnowski, Na: Nagano, PF: Ptitsyn-Finkelstein, NO: Nisikawa-Ooi, GGR: Gibrat-Garinier-Robson. They were chosen from eight different methodologies, on the basis of their performance using test structures. In the New Joint Method, Na method has been replaced by SSthread (Prediction of protein Secondary Structure using Threading). Since the different predictions are computed independently, the New joint method is well suited for parallel computing.

References :

K. Nishikawa and T. Noguchi :
"Predicting protein secondary structure based on amino acid sequence",
Methods in Enzymology, Vol.202, pp.31-44 (1991).

M. Ito, Y. Matsuo and K. Nishikawa :
"Prediction of protein secondary structure using the 3D-1D compatibility algorithm.",
Comput. Appl. Biosci. vol.13, pp.415-424 (1997).

How to use :

See 'Service status' and confirm the service is ON.
Select 'Method'.
Chou-Fasman and New Joint are available.
- Chou-Fasman : very popular and fast to calculate but tends to be less accurate.
- New Joint : a combination of several prediction programs, therefore very heavy.
Enter any label for your query into the field 'Query label='. (Optional)
Paste your amino acid sequence into the text area 'Cut and Paste Your Sequence here'.
Two formats are acceptable.
4.1
Simple amino acid sequence ( single-letter amino acid code format ) is acceptable.
Example :
```
KLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVTEYMSKGSLLDFLK
```
4.2
Fasta format is acceptable.
Example :
```
>CSRC_HUMAN
KLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVTEYMSKGSLLDFLK
```
( If the field 'Query label=' is blank, the label after '>' in the first line will be used as the label for the sequence. Any spaces or any characters mustn't be put before '>'. )
Maximum length is 500 residues. Results obtained for sequences shorter than 50 residues are not reliable.
Press the 'Service status' button to confirm the service status for your query.
If you want to reset the input form Press 'Reset this form'.
Then, press 'Submit' button to submit your query to the server.
Results Example

Copyright Notice :

Copyright of the original New Joint Method and COMPASS program used in the SSthread by Protein Engineering Research Institute (PERI). The new version of the New Joint Method has been parallelized by Real World Computing Partnership (RWCP). All rights reserved. For further information, please contact to Tamotsu Noguchi, Real World Computing Partnership,Parallel Application Laboratory, Tsukuba Research Center, Tsukuba Mitsui Bldg., 1-6-1 Takezono, Tsukuba 305, Japan.
TEL:81(298)53-1707, FAX:81(298)53-1680, E-mail:noguchi@trc.rwcp.or.jp.

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