Parameters for profile-profile comparison:

• Weight for amino acid scores:  
  
• Weight for predicted secondary structure scores:  
  

Parameters for deriving sequence profiles from PSI-BLAST searches:

• PSI-BLAST iteration number:  
  
• PSI-BLAST e-value inclusion threshold:  
  
• Identity cutoff below which distant homologs are removed:  
  
• Maximum number of homologs kept for PSI-BLAST alignment:  
  

Parameters for detecting and using homologs with 3D structures (homolog3d):

• PSI-BLAST e-value cutoff against structural database:  
  
• Identity cutoff below which 3D structures are not used:  
  
• Align homologs with 3D structures by programs:  
• DaliLite
• FAST
• TM-align


• Realign target-homolog3d using profile-profile alignment:  

Parameters for pairwise alignments between input 3D structures:

• Align input structures by programs:  
• DaliLite
• FAST
• TM-align

Parameters for aligning sequences within groups in the first alignment stage:

• Align sequences within groups in the first alignment stage by:  
• MAFFT (fast)
• PROMALS (slow but could be more accurate)