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PREDITOR


 

PREDITOR Help Wishart lab

PREDITOR is a program for PREDIcting φ, ψ, χ1, and ω TORsion angles in proteins  from 13C, 15N and 1H chemical shifts and sequential homology. PREDITOR's accuracy in predicting φ and ψ is close to 90%. The average χ1 accuracy is 84% while the ω accuracy is 99.98% for trans peptide bond identification and 93% for cis peptide bond identification. Overall, the program is 35X faster and its predictions are approximately 20% better than existing methods. You can find additional information about PREDITOR protocol on...

Please cite:  Berjanskii MV, Neal S, Wishart DS. PREDITOR: a web server for predicting protein torsion angle restraints. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W63-9.

Basic usage
Select the format of the input file: BMRB NMR-STAR (Example)
SHIFTY (Example)
FASTA (Example)
Upload chemical shift file
OR
Paste chemical shifts into the text box below:
IMPORTANT: If a file is selected for upload above, it will be used and content of the text box below will be ignored.
   

 

Advanced options
 
Initial steps:
yes no Re-reference chemical shifts
yes no Only display PDB homologues
 
Predict dihedral angles using BMRB/SHIFTY input and...
 Chemical shifts and a PDB homologue (Default)
 Chemical shifts only
 A PDB homologue only
 Chemical shifts and a homologous protein of your choice
     - if you use the last option, enter PDB ID or PDB ID & chain letter  (Example)
Only homology-based predictions will be run for FASTA input regardless selection of advanced options listed above
 
In addition to predicted angles, output...
yes no X-PLOR/CNS torsion angle restraints
yes no CYANA/AMBER torsion angle restraints
yes no Re-referenced chemical shifts
yes no Predictions of secondary structure using Chemical Shift Index (CSI)
yes no Predictions of protein flexibility using Random Coil Index (RCI)
yes no PDB homologues
 
   

 

Problems? Questions? Suggestions? Please contact: Mark Berjanskii or the Canadian Bioinformatics Help Desk
PREDITOR database is DB 1.0 (141 proteins, built on April 10th, 2006)

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