COUDES: Supplementary Data
You will find on this page some supplementary information about COUDES:
Find here the list of chains for the:
- database of 426 chains: click here
BEWARE (Nov 06 2007): there are some obsolet files in EXTR426 that have been updated in PROM426; some of them has become obsolet since then.
EXTR426 PROM426 UPDATE(since then)
3b5c 1cyo -
5icb 1ig5 -
1alo 1hlr 1vlb
- database of 547 chains: click here
- database of 823 chains: click here
Find here the sequences and turns assigned by either extract_turn or PROMOTIF:
- database of 426 chains:
- database of 547 chains:
- database of 823 chains:
For each chain you find :
- the fasta sequence: the first line is a commentary, the second line is the sequence without any carriage return)
- the list of turns formatted as follows: each number is affected to the tetrapeptide starting at the same position in the sequence (as in COUDES output), with the following code:
- '0' -> no turn
- '1' -> type I
- '2' -> type II
- '3' -> type VIII
- '4' -> type I'
- '5' -> type II'
- '6' -> type IV
Find here the propensities calculated from the:
- database of 426 chains using:
- database of 547 chains using:
- database of 823 chains using:
Here is the global accuracy of COUDES prediction calculated on a seven-fold cross validation on the database PROM426:
|turn / non turn
- MCC = Matthews Correlation Coefficient
- Qtotal = percentage of correct prediction
- Qobs = fraction of residues observed in beta-turn that are correctly predicted
- Qpred = fraction of residues predicted in beta-turn that are correct
For further details, please see Fuchs & Alix (2005).
You will find here the supplementary figures related to COUDES article [Fuchs 2005] :
- Supplementary Figure 1: ROC curves of COUDES (with or without secondary structure information, and with or without PSSM) with fixed m and PSIthreshold. Each plot has been obtained by varying Sthreshold but with m=4 and PSIthreshold=0 (see Kaur & Raghava (Protein Science, 2003) for a definition of sensitivity and specificity).
- Supplementary Figure 2: ROC curves of COUDES (with or without secondary structure information, and with or without PSSM) whatever the value of m and PSIthreshold.
The red plots were obtained by varying Sthreshold, m and PSIthreshold. The black plots were obtained by varying Sthreshold but with fixed m and PSIthreshold. (m=4 and PSIthreshold=0, like in supplementary figure 1).
- Fuchs PFJ, Alix AJP (2005). High accuracy prediction of beta-turns and their types using propensities and multiple alignments. Proteins: Struct. Funct. Bioinf., 59, 828-839.
- Kaur H, Raghava GP (2003). A neural-network based method for prediction of gamma-turns in proteins from multiple sequence alignment. Protein Sci., 12, 627-634.
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