Pagal

Pagal analyzes alpha-helical properties in protein structures to compute hydrophobic moments and assess structural features relevant to antimicrobial peptides.

Key Features:

• Hydrophobic Moment Calculation: Computes the hydrophobic moment of alpha helices to assess amphipathicity and residue alignment on helix surfaces.
• Visualization Scripts: Generates Edmundson wheels and high-resolution graphics for alpha helices using TikZ and PyMOL.
• Color-Coded Surface Generation: Produces color-coded protein surface representations to illustrate structural properties.
• Empirical Structural Validation: Validates an empirical geometric property relating distances between Cα atoms of the ith and (i+4)th residues and their carbonyl oxygens using 100 non-homologous high-resolution structures from the PISCES database.
• Output File Compatibility: Produces input/output files compatible with TikZ and PyMOL for downstream visualization.

Scientific Applications:

• Antimicrobial Peptide Analysis: Characterizes alpha-helical features and hydrophobic moments that influence antimicrobial peptide function.
• Peptide Design and Optimization: Provides structural metrics and visualizations to inform design and optimization of helical peptide candidates for therapeutic applications.

Methodology:

Computes hydrophobic moments and generates Edmundson wheels and color-coded surfaces via TikZ and PyMOL; validates the Cα(i)–Cα(i+4) and carbonyl oxygen distance property by analyzing 100 non-homologous high-resolution structures from the PISCES database and reproducing previously described computational techniques; outputs are compatible with TikZ and PyMOL.