ProDy Tutorial

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Tutorial files: ZIP TGZ

• Introduction
  • Structural Ensemble Analysis
  • Elastic Network Models
  • Trajectory Analysis
  • Visualization
• How to Start
  • Using ProDy
  • Interactive Usage
  • Using Documentation
• ProDy Basics
  • File Parsers
  • Analysis Functions
  • Plotting Functions
  • Protein Structures
  • Atom Groups
  • ProDy Verbosity
• Atom Groups
  • Building an Atom Group
  • Storing data in AtomGroup
• Atom Selections
  • Atom Selections
  • Operations on Selections
• Hierarchical Views
  • Hierarchical Views
  • Chains
  • Residues
  • Atoms
  • State Changes
• Structure Analysis
  • Measure geometric properties
  • Compare and align structures
  • Writing PDB files
• Dynamics Analysis
  • PCA Calculations
  • ANM Calculations
  • Comparative Analysis
  • Output Data Files
  • External Data
  • Plotting Data
  • More Examples
• Sequence Analysis
  • Access Pfam
  • Parse MSA
  • Sequences
  • Analysis
• Applications Tutorial
  • Align PDB files
  • ANM calculations
  • PCA calculations

Acknowledgments

Continued development of Protein Dynamics Software ProDy and associated programs is partially supported by the NIH-funded R01 GM139297 entitled “Toward a deeper understanding of allostery and allotargeting by computational approaches”.