If you use this service, could you please send us a mail to npsang@ibcp.fr with details about your usage of the NPSA service (tools used, frequency, type of sequence, ..) ? Could you explain what makes this service unique for you ? Could you please add information about your country and your laboratory ? Thanks

DPM help

A brief introduction to DPM
DPM (Double Prediction Method) is a secondary structure prediction which predicts the protein structural class and then the secondary structure for the sequence (this is why Double). The DPM method consists in 4 successive steps:

Prediction of the structural class of a protein from AA composition (Nakashima et al. 1986 J. Biochem. Tokyo, 99, 153-162).
Preliminary secondary structure estimation from a simple algorithm.
Comparison between the 2 independent predictions.
Optimization of parameters and reprediction of secondary structure.

NPS@ is the orginal server for this method.

Availability in NPS@
This method is available :

At URL : https://npsa-prabi.ibcp.fr/NPSA/npsa_dpm.html.
In secondary consensus prediction at URL : https://npsa-prabi.ibcp.fr/NPSA/npsa_seccons.html.
In protein sequences multiple alignement at URLs :
- CLUSTALW : https://npsa-prabi.ibcp.fr/NPSA/npsa_clustalw.html
- MULTALIN : https://npsa-prabi.ibcp.fr/NPSA/npsa_multalin.html
when you work with a sequence in NPS@ if you make a consensus secondary prediction on it.

Parameters
No parameter required.

NPS@ DPM output example
You can see:

MPSA/ANTHEPROT link to view the prediction in these local protein sequence analysis softwares.
The color coded prediction (a sequence line and below the corresponding predicted states).
The sequence length.
The percentage of each secondary element.
Two graphics. The first to better visualize the prediction. In the second, there are the score curves for each predicted state.
Links on the prediction result text file.

References

User : public Last modification time : Mon Mar 15 15:24:36 2021. Current time : Sun Oct 13 06:24:14 2024