MD-TASK documentation

Getting started

• Introduction
  • Contribute
  • Citing MD-TASK
  • License
• Installation
  • Platform compatibility
  • Install system dependencies
  • Download the project
  • Install Python dependencies
  • Install R dependencies

Usage

• General
  • Activating the virtual environment
  • Add MD-TASK to your PATH
  • Trajectory vs Topology
  • Reducing your trajectory
  • Test Data
  • Logging
• Network Analysis
  • Measurements
  • Calculating BC and L
  • Calculating ΔL
  • Calculating ΔBC
  • Calculating Average BC and L (and standard deviation)
  • SNP Analysis - wild-type vs mutant trajectories
  • SNP Analysis - wild-type vs mutants heatmap
  • SNP Analysis - residue contact map
• Pertubation Response Scanning
  • Performing PRS
• Dynamic Cross-Correlation
  • Calculating dynamic cross-correlation