AnglerFish

AnglerFish calculates orientations of α-helices in rotationally symmetric membrane protein structures, such as channels and transporters, to quantify tilt and swing angles for comparative analysis of conformational states.

Key Features:

• Helix Orientation Parameters: Computes helix orientation using the primary angles 'tilt' and 'swing' to define spatial arrangement of transmembrane α-helices.
• State Comparison: Analyzes structural changes between different protein states, accommodating both symmetric and asymmetric transitions.
• Quantitative Comparison: Enables quantitative comparisons between related structures and between distinct subunits within the same complex.
• Input Format: Operates on Protein Data Bank (PDB) coordinate files to derive orientation metrics.
• Implementation: Implemented using Perl-cgi and deployed under Apache.

Scientific Applications:

• Drug Discovery: Inform design of molecules targeting specific conformational states by quantifying helical dynamics relevant to ligand binding and gating.
• Protein Engineering: Provide orientation data to guide rational design of protein variants with altered functional properties.
• Structural Biology: Support comparative analyses of membrane protein structures from crystallography and cryo-electron microscopy to elucidate functional mechanisms.

Methodology:

Uses Protein Data Bank (PDB) coordinates to parameterize helical angles (tilt and swing) and computationally translate structural coordinates into orientation metrics.