Drug design module (DRUG)

• Introduction.
• Reading/writing drugs from/into drug coordinate files
  • Reading cambridge database files (GETCSD)
  • Reading TRIPOS MOL2 files (GETML2)
  • creating a small molecule topology entry (DRGTOP)
• Drug docking options
  • Dock with WHAT IF's shitty docker (WIDOCK)
  • Dock with WHAT IF's shitty docker (DCKOPT)
  • Dock with WHAT IF's manual docker (MANDCK)
  • docking a drug (LIGIN)
  • Docking flexible drugs with (FLEXX)
    • Prepare files for FLEXX (INIFLX)
    • Prepare files for FLEXX (ANIFLX)
• Interaction with the RELIWE drug docking database
  • DOCKDB Substructure search via smiles-code (SUBSTR)
  • DOCKDB Substructure search via fragment name (SUBFRA)
  • DOCKDB Find pairs of contacting residues (FNDCAA)
  • DOCKDB Find (and display) a PDB file (FNDPDB)
  • DOCKDB List of searchable PDB files (LSTDDB)
  • DOCKDB Initialize for DOCKDB usage of FLEXX (GETFLX)
  • DOCKDB Load file from database (GETDDB)
  • DOCKDB Demonstration command (FNDCPX)
  • DOCKDB interactive VQL query (DDBVQL)
  • DOCKDB gets started (do first, but only once) (INIDDB)