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These algorithms are for the prediction of
1) alpha helices and beta strands that can turn to random coils;
2) alpha helices, beta strands, and random coils that can turn to intrinsically disordered state;
3) random coils that can turn to alpha helices and beta strands;
4) secondary structure of a protein that has been renaturated from the random coil state (PentUnFOLD 2D and PentUnFOLD 1D trough the web server).
The algorithms work with PDB file, the output of the DSSP algorithm, and the output of the PIC server (PentUnFOLD 3D).
Also the PentUnFOLD 2D and the PentUnFOLD 1D trough the web server can work with just an amino acid sequence.
Instructions are written in each list of the MS Excel table.
Please, follow them in "left to right" direction.
On the "Results" list one will see the table containing predictions in text format.
There are several columns:
1) user input for AA: you can insert amino acid residues in one-letter code against a certain position;
2) user input for SS: you can insert secondary structure in one-letter code against a certain position;
3) AA: predictions made by amino acid scale;
4) WO: predictions made by pentapeptide scale;
5) HELIX: description of alpha helices - HS means stable alpha-helical residue that should not turn to random coil, HN means nonstable alpha-helical residue that is prone to turn to random coil;
6) SHEET: description of beta strand - ES means stable beta-strand residue that should not turn to random coil, EN means nonstable beta-strand residue that is prone to turn to random coil;
7) Disordered coil: D means residue that is prone to turn to disordered state, C means residue that is prone to stay in random coil, CH means residue that is prone to form alpha helix, CE means residue that is prone to form beta strand;
8) Disordered helix: D means residue that is prone to turn to disordered state;
9) Disordered sheet: D means residue that is prone to turn to disordered state.
On the "Self predictions" list of the PentUnFOLD 2D one will see same columns, but for a self-predicted secondary structure.
That secondary structure is predicted according to the hypothesis that all elements of secondary structure are formed from the random coil state.
On the "3D results" list of the PentUnFOLD 3D one can see predictions for just disordered "D" and ordered "O" residues.
On the "Contacts" list of the PentUnFOLD 3D one can see the table with the numbers of contacts of each residue with completely disordered (V), disordered (D), nonstable (N), and stable (S) residues.
Completely disordered residues are predicted by the PentUnFOLD 3D algorithm on the "Results" list.