March 26th, 2001

Energy of helical windows

• Explanation to come

Position dependence

• Explanation to come

October 12th, 1998

N-term Pro Box

• A local motif at the N-term of helices, involving a Pro at the Ncap position and three hydrophobic residues at positions N', N3 & N4. The pattern (Pro + hydrophobic residues) contributes to helix stability and defines the N terminus.

Agadir1s-2

The new version is a modification of AGADIR1s (Biopolymers 41, 495-509).

Update of the calculation

• The residues after the N- and C-terminal blocking groups can adopt an helical confomation.
• Local motifs at the N- and C-termini (Hydrophobic staple, Capping box, Schellman motif and Pro-capping motif) are included.
• Long range electrostatics (up to 20 residues apart), are considered using the Debye-Huckel approximation.
• The ionic strenght dependence on helix stability is included.

Update of the output

• Some NMR parameters are predicted: CaH conformational shifts and J3aN coupling constants.
• The screening of solvent conditions (pH, temperature and ionic strength) for a particular peptide sequence is possible.