PentaFOLD 3.0
This algorithm is for prediction of stable, semi stable, and nonstable fragments of alpha helices, beta strands, and random coils in 3D structures of proteins.
The algorithm works with PDB file and the output of the DSSP algorithm.
Instructions
Instructions are written in each list of the MS Excel table.
Please, follow them in "left to right" direction.
Results
On the "Predictions" list one will see the table containing predictions in text format (H, E, or C).
There are several columns:
1) The number of amino acid residue according to PDB file
2) Amino acid residue in one-letter code
3) Prediction made by the alpha helical pattern (in favor of alpha helices);
4) Prediction made by the beta structural pattern (in favor of beta strands);
5) Secondary structure according to the DSSP
6) Stable residues in alpha helices
7) Stable residues in beta strands
8) Semi stable residues in alpha helices
9) Semi stable residues in beta strands
10) Stable residues from random coils
11) Semi stable residues from random coils
On the "mono" list one will see predictions by the original amino acid propensity scale in numbers.
On the "monocoil" list one will see predictions by the new amino acid scale that distinguishes 4 types of random coils in numbers and in comparison with DSSP.
On the "pentapeptide" list one will see predictions by the original pentapeptide propensity scale in numbers.
On the "pentacoil" list one will see predictions by the new pentapeptide scale that distinguishes 4 types of random coils in numbers and in comparison with DSSP.
Probability scales can be found on corresponding lists.