Interactions and Stability (InSty) analysis

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• Introduction
  • Required Programs
  • Recommended Programs
  • Getting Started
• Interactions/Stability Evaluation
  • Analysis of interactions for a single PDB structure
  • Compute all types of interactions
  • Visualize interactions in VMD
  • Additional selections
  • Change selection criteria for interaction type
  • Assess the functional significance of a residue
  • Energy of interactions
  • Visualize number of interactions onto 3D structure
  • Exclude some interaction types from calculations
• PDB structure without hydrogens
  • Add missing hydrogen atoms to the structure
• PDB structure with multiple chains
  • Add missing hydrogen atoms to the structure
  • Perform InSty calculations and extract chain-chain interactions
  • Compute Interactions
  • Select interactions between chains
  • Set only interactions between chains
• Extract chain-chain interactions in ensemble or trajectory analysis
• Ensemble PDB analysis
  • Parse structure
  • Compute interactions for an Ensemble PDB
  • Select particular frames or change the default parameters of the interactions
  • Compute all types of interactions at once
  • Selection of protein regions and conformations
  • Import previously saved file with interactions
  • Change selection criteria for interaction type
• Trajectory analysis
  • Parse trajectory
  • Compute all availabe types of interactions
  • Change selection criteria for interaction type
  • Statistics
  • Compare two independent frames
  • Parse previously saved data
• Signature Interactions of ensembles
  • BLAST approach
  • Dali approach
  • Foldseek approach

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”.