Knot_pull

Knot_pull performs automated smoothing and topological analysis of 3D biopolymer structures to simplify configurations and detect knots, links, and slipknots in proteins, RNA, and chromatin chains.

Key Features:

• Topology simplification: Generates a smoothing trajectory to reduce geometric complexity while preserving the topology of biopolymers.
• Knot detection: Identifies and classifies knot types and related topological features, including links and slipknots when subchains are designated.
• Format compatibility: Supports PDB, CIF, and XYZ file formats used in structural biology.
• Python compatibility: Runs under Python version 2.7 or higher.
• Visualization support: Provides a wrapper script for PyMOL to visualize smoothed structures and detected topological features.

Scientific Applications:

• Protein research: Detection and classification of knots in protein structures to inform studies of folding, stability, and function.
• RNA studies: Analysis of knotting in RNA molecules to investigate structural dynamics and potential regulatory roles.
• Chromatin analysis: Examination of topological arrangements in chromatin chains to study genomic organization and its implications.

Methodology:

Generates an iterative smoothing trajectory that refines input 3D biopolymer structures to reduce complexity while preserving topological features and applies its algorithm to identify knots, links, and slipknots.