• PRABI-GERLAND
  RHONE-ALPES BIOINFORMATIC POLE GERLAND SITE
• Institute of Biology and Protein Chemistry

• Home
• Teaching
• Publications
• Links
• Contact

A brief introduction to GOR1
GOR1 (GARNIER OSGUTHORPE and ROBSON) is a secondary structure prediction method based on the information theory. Scores for 4 conformational states are computed on a sliding window of 17 residues. These scores are corrected by decision constants and the highest one gives the conformational state for the residue in the center of the window (9th position).

Availability in NPS@
This method is available :

• At URL : https://npsa-prabi.ibcp.fr/NPSA/npsa_gor.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
You can set the decision constants. You can choose the auto-calculated option or you can type your own decision constants (The default ones are the optimized ones).

NPS@ GOR1 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.
• The paramaters used.
• Link on the prediction result text file.

References