Structure Analysis

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• Introduction
  • Required Programs
  • Recommended Programs
  • Getting Started
• PDB files
  • Fetch PDB files
  • Parse PDB files
  • Write PDB file
• Blast Search PDB
  • Blast search
  • Best match
  • PDB hits
  • Download hits
• Building Biomolecules
  • Build a Multimer
  • Build a Tetramer
• Alignments
  • Parse an NMR structure
  • Calculate RMSD
  • Align coordinate sets
  • Write aligned coordinates
• Structure Comparison
  • Match chains
  • Map onto a chain
• Intermolecular Contacts
  • Simple contact selections
  • Contacts between different atom groups
  • Composite contact selections
  • Spherical atom selections
  • Fast contact selections
• Ligand Extraction
  • Parse reference and blast search
  • Align structures and extract ligands

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”.