Pagal

Pagal is a software tool that provides computational methods to analyze alpha helices (AH) in proteins, focusing on quantifying their amphipathic nature. Key features of Pagal include:

1. Calculating the hydrophobic moment of AHs, which measures the amphipathicity by quantifying the alignment of hydrophobic residues on one surface and charged residues on the other.

2. Input files for TikZ, a package for creating high-resolution graphics, are generated to visualize the Edmundson wheel and display the direction and magnitude of the hydrophobic moment.

3. Creation of Pymol scripts to generate color-coded protein surfaces, aiding in the visualization of the amphipathic nature of AHs.

4. Validation of an empirical structural property of AHs, where the distance between the Cα atoms of the ith and (i+4)th residue is equal to the distance between the carbonyl oxygens of the ith and (i+4)th residue, using 100 non-homologous high-resolution structures from the PISCES database.