Protein Runway

Protein Runway is a tool for the schematic visualization of large molecules’ most important movements based on computational analysis. It consists of:

• A snakemake pipeline that takes a topology and trajectory. It outputs a PDB with a simplified trajectory visualizing its normal modes and a TSV file with various potential segmentations of the protein.

• An object-oriented library that encapsulates the specific processing logic that the workflow applies.

• A blender extension that visualizes the results.

Contents:

• Introduction
• Installation
  • Setup snakemake workflow
  • Run snakemake workflow
  • Build blender extension
• Usage
  • Visualization Demo
• Blender extension
  • Main panel
  • Importing the static structure
  • Animating the trajectory
  • Choosing the segmentation
• API Reference
  • util
  • trajectory
  • normal_modes
  • segmentation