Ensemble Analysis

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• Introduction
  • Required Programs
  • Recommended Programs
  • Getting Started
• NMR Models
  • Notes
  • Prepare ensemble
  • PCA calculations
  • Write NMD file
  • Print data
  • Compare with ANM results
• Homologous Proteins
  • Setup
  • Parameters
  • Blast and download
  • Set reference
  • Prepare ensemble
  • Align PDB files
  • Perform PCA
  • Plot results
• Heterogeneous X-ray Structures
  • Calculations
  • Analysis
  • Plotting
  • Visualization
• Multimeric Structures
  • Input and Parameters
  • Prepare Ensemble
  • Use buildPDBEnsemble Function
  • Perform PCA
  • Plot results

Acknowledgments

Continued development of Protein Dynamics Software ProDy and associated programs is partially supported by the NIH-funded Biomedical Technology and Research Center (BTRC) on High Performance Computing for Multiscale Modeling of Biological Systems (MMBios) (P41 GM103712).