AMIGOS III

AMIGOS III performs visualization and comparative analysis of nucleic acid tertiary structure using pseudo-torsion angle representations to enable motif identification across RNA and DNA.

Key Features:

• Pseudo-torsion angle representation: Uses a reduced model that assigns each nucleotide a pair of pseudo-torsion angles (eta and theta or eta' and theta').
• Angle definitions: Defines eta and theta using P and C4' atoms and eta' and theta' using P and C1' atoms.
• Per-nucleotide calculations: Calculates eta, theta, eta' and theta' for each nucleotide in input structures.
• RNA and DNA support: Parses and analyzes both RNA and DNA structures using the pseudo-torsion framework.
• PyMOL integration: Produces enhanced 3D representations and pseudo-torsion angle visualizations within PyMOL.
• Worm database generation: Generates nucleic acid "worm" databases and provides visualization of these worms.
• Motif search capability: Enables motif searches based on pseudo-torsion angle comparisons across nucleic acid types.
• Tertiary structure input handling: Facilitates preparation and interpretation of tertiary structure inputs for pseudo-torsion analysis.

Scientific Applications:

• Motif discovery: Identification of nucleic acid motifs via pseudo-torsion angle-based searches in RNA and DNA.
• Comparative structural analysis: Comparative analysis of nucleic acid motifs using reduced torsional parameter space (eta/theta or eta'/theta').
• Structural interpretation: Visualization of pseudo-torsion angles in 3D to aid interpretation of tertiary structural motifs.
• Database-driven analysis: Use of nucleic acid worm databases to accelerate motif-based structural searches.

Methodology:

Computes pseudo-torsion angles (eta, theta from P and C4'; eta', theta' from P and C1') per nucleotide, generates nucleic acid worm databases, performs motif searches using pseudo-torsion angle comparisons, and outputs visualizations via PyMOL.