forgi

forgi analyzes RNA tertiary structures by converting secondary structure elements such as stems, bulges, and loops into coarse-grained 3D representations to enable analysis of tertiary geometry and interactions.

Key Features:

• Secondary Structure Element Representation: Models stems, bulges, and loops as coarse-grained elements by fitting a cylinder to the helix axis and converting those elements into 3D structures.
• Integration with Biopython: Incorporates all-atom 3D information via Biopython to relate coarse-grained elements to atomic coordinates.
• Versatile File Format Support: Accepts dot-bracket strings and atomic structure files including PDB and MMCIF formats for input.
• Handling Complex Structures: Supports modified residues, missing residues, cofold and multifold configurations, and arbitrary nucleotide numbering.

Scientific Applications:

• Stacking Helix Analysis: Analyzes stacking helices within junctions and pseudoknots and quantifies deviations from ideal coaxial geometries.
• RNA Folding and Stability Assessment: Provides structural metrics that inform on the stability and functional implications of RNA tertiary arrangements.

Methodology:

Uses a coarse-grained approach that models secondary structure elements as cylinders aligned to fitted helix axes, and integrates Biopython-derived all-atom 3D coordinates.