Messages:

- MC-Fold CPU time is currently limited to 12 hours per job.
- MC-Fold sequence length is limited to 150 nucleotides.
- Linux executable version without limits available here.

Pipeline page MC-Fold's user's guide


MC-FOLD

 1. Sequence  
    

         

 2. Algorithm (Option) 

  • Consider H-type pseudoknots

  • Return the best structures

  • Explore the best % sub-optimal structures

    Sequence name
    


 3. Structural Constraints (Option) 

  • Use '(' and ')' for paired nucleotides
  • Use '.' for unpaired nucleotides
  • Use '*' for unconstrained nucleotides (paired or unpaired)

    Structural mask
    

    Convert all unpaired nucleotides to unconstrained


 4. Single-Stranded Chemical/Enzymatic Reactivity Data (Option) 

  • Use 'x' or 'X' to indicate reactive nucleotides
  • Use '.' to indicate unreactive,
    or different reactivity intensities (in multiple mask mode)

    High reactivity mask (+8 kcal/mol penalty)
    

    Medium reactivity mask (+4 kcal/mol penalty)
    

    Low reactivity mask (+2 kcal/mol penalty)
    
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