Signature Dynamics

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• Introduction
  • Required Programs
  • Getting Started
  • How to Cite
• Overview
  • Prepare ensemble (using Dali)
  • Mode ensemble
  • Signature dynamics
  • Spectral overlap and distance
  • Comparing with sequence and structural distances
• Data Collection with CATH
  • Navigating the CATH tree
  • Searching CATH
  • Getting atomic structures from CATH and building ensembles
• Data Collection with PDB IDs
  • Prepare ensemble
• Core Calculations
  • Mode Ensemble
  • Signature Dynamics
  • Saving the ModeEnsemble
• Classification using sequence, structure and dynamics distances
  • Load PDBEnsemble and ModeEnsemble
  • Spectral overlap and distance
  • Sequence and structural distances
  • Comparing sequence, structural and dynamic classifications

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”.