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4. Methods 2 - Using special features

The use of auxiliary constraints to force computed foldings to agree with experimental data or preconceived notions was first introduced in [11]. Because the current program computes a selection of optimal and suboptimal structures, and the energy dot plot displays all possible helices that might be contained in close to optimal foldings, there is less of a need to constrain a folding. If an optimal folding conflicts with experimental data, perhaps a suboptimal one will be better. Nevertheless, the current programs, lrna and crna, both have the same ability to use auxiliary information as the earlier single fold program [21].

The use of special sequence characters to designate bases susceptible to single-stranded nuclease cleavage has already been discussed in 3.6. The special features can be selected when the ``main menu'' (3.10):

          1  Energy Parameter           6  Single Prohibit
          2  Single Force               7  Double Prohibit
          3  Double Force               8  Begin Folding  
          4  Closed Excision            9  Show current   
          5  Open Excision             10  Clear current  

 Enter Choice
is displayed. The choices are selected by number.

Michael Zuker
Thu Nov 2 14:28:14 CST 1995