ProDy Manual

Welcome to the official ProDy documentation. You can read these pages in PDF format too.

• Installation
  • Required Software
  • Quick Install
  • Installing From Source (not recommended)
  • Recommended Software
  • Included in ProDy
  • Source Code
• Applications
  • ProDy Applications
  • Evol Applications
• Reference Manual
  • Atomic Data
  • Chromatin Dynamics Analysis
  • Compounds Analysis
  • Database Support
  • Dynamical Domain Decomposition
  • Dynamics Analysis
  • Ensemble Analysis
  • KDTree
  • Measurement Tools
  • Protein Structure
  • Sequence Analysis
  • Trajectory I/O
  • ProDy Utilities
  • Applications API
  • Configuration & Logging
• Developer’s Guide
  • Contributing to ProDy
  • Documenting ProDy
  • How to Make a Release
  • Style Guide for ProDy
  • Testing ProDy
  • Writing Tutorials
  • Building the Website
  • Making Windows Installers
  • Cross-platform Issues
• Release Notes
  • ProDy 2.5 Series
  • ProDy 2.4 Series
  • ProDy 2.3 Series
  • ProDy 2.2 Series
  • ProDy 2.1 Series
  • ProDy 2.0 Series
  • ProDy 1.11 Series
  • ProDy 1.10 Series
  • ProDy 1.9 Series
  • ProDy 1.8 Series
  • ProDy 1.7 Series
  • ProDy 1.6 Series
  • ProDy 1.5 Series
  • ProDy 1.4 Series
  • ProDy 1.3 Series
  • ProDy 1.2 Series
  • ProDy 1.1 Series
  • ProDy 1.0 Series
  • ProDy 0.9 Series
  • ProDy 0.8 Series
  • ProDy 0.7 Series
  • ProDy 0.6 Series
  • ProDy 0.5 Series
  • ProDy 0.2 Series
  • ProDy 0.1 Series
• About ProDy
  • People
  • Citing
  • Credits
  • Funding
  • License

• Index

• Module Index

• Search Page

Release:

2.5.0

Date:

May 24, 2026