The structure fragment database (DGLOOP)

• Introduction.
• Implications of the algorithm
• Searching in the database
  • Finding stretches (DGFIND)
  • Inserting residue(s) using the database (DGINS)
  • Inserting residue(s) using the database (DGINSS)
  • Finding alternative conformations (DGFIX)
  • Mutating using the database (DGMUT)
• Look alike contacts DGCONT
• Replacing a residue with a hit (DGREP)
• Display fragments
  • Movie of fragments (DGGRA)
  • Showing all fragments at once (DGGRAL)
  • Listing hits (DGSHOW)
• Working with alpha carbons only
  • Builing a structure from alpha carbons (CATOAL)
  • Keeping only alpha carbons (ALTOCA)
• Rotamer searches
  • Single rotamer searches (DGR1-1)
  • Single rotamer searches (DGROTA)
  • Multiple residue rotamers at one position (DGRN-1)
  • One residue type rotamer for a range of residues (DGR1-N)
  • All rotamers for a residue range (DGRN-N)
  • Self rotamers (DGRSLF)
  • geometric best rotamers for a residue range (DGRS-N)
• Fragment group administration
  • Resetting the group length (LENSET)
  • Initializing the groups (GRPINI)
  • Showing the search groups (GRPSHO)
• Parameter related option
  • Tightening the parameters (TIGHT)
  • Relaxing the parameters (RELAX)
  • Resetting the default parameters (RESPAR)
  • Showing dgloop parameters (SHOPAR)
  • Parameters (PARAMS)
    • Maximal Ca-Ca distance misfit allowed (DGCERR)
    • Allowed RMS fit error (DGTERR)
    • Maximal Ca misplacement after real suppos (MXCAER)
    • Maximal number of hits to be searched for (DGSHWT)
    • Additional backbone fit flag (ADDFIT)
    • Number of anchoring residues around insertions (INANCH)
    • Should accessibility constraints be used (USEACC)
    • Lower limit on accessibility of database hit (LOWACC)
    • Lower limit on accessibility of database hit (HGHACC)
    • Maximal error in DGCONT option (CNTERR)
• Automatic mutant prediction
• Statistics on groups of hits