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4.1 Energy Parameter

When this selection is made, a secondary menu appears:

             Energy Parameters (10ths kcal/mole)

           1 Extra stack energy                        [    0]
           2 Extra bulge energy                        [    0]
           3 Extra loop energy (interior)              [    0]
           4 Extra loop energy (hairpin)               [    0]
           5 Extra loop energy (multi)                 [   46]
           6 Multi loop energy/single-stranded base    [    4]
           7 Maximum size of interior loop             [   30]
           8 Maximum lopsidedness of an interior loop  [   30]
           9 Bonus Energy                              [ -500]
          10 Multi loop energy/closing base-pair       [    1]

 Enter Parameter to be changed            
                                       (<return> for main menu)
This menu displays the user adjustable ``energy'' parameters, with their current values within the square brackets. The values shown above are the defaults. The user enters a desired number and is then prompted for a new value for the selected parameter.

The ``Extra stack energy'' is a user defined energy that is added to all stacked base pairs. This could be used in conjunction with user defined energy files containing energy values that are all 0. This would have the effect of giving an equal weight to all base pairs so that the program would then be optimizing the number of base pairs. Items 2 through 4 are extra energies that can be assigned to all bulge, interior and hairpin loops, respectively. Increasing the penalty for bulge, interior or hairpin loops will tend to produce foldings with fewer such loops.

Energy parameters 5, 6 and 10, denoted by a, b and c, respectively, are used to assign energies to multi-branched loops. A multi-branched loop with n1 single-stranded base pairs and n2 helices branching off from it is assigned an energy of a + bn1 + cn2. These simple assignments are in lieu of measured quantities or thermodynamic calculations. The default values have been chosen to optimize folding predictions for a number of sequences whose structure is known from phylogenetic comparisons [15].

If an interior loop has m1 single-stranded bases on 1 side and m2 single-stranded bases on the other, then energy parameters 7 and 8 are upper bounds for m1 + m2 and |m1 - m2|, respectively. These parameters also apply to bulge loops, where min{m1,m2}. The default value for parameter 7 is 30. This should be sufficient for folding at the default temperature of 37° C, but might have to be raised for folding at elevated temperatures where very large interior loops might be expected. Setting this parameter to a smaller number will decrease folding times while increasing the risk of missing the optimal folding. The user can also experiment with the ``lopsidedness'' parameter to force foldings to have better balanced interior loops.

Energy parameter 9 is the ``bonus energy'' that is used by the program to force certain bases to be double-stranded or to force certain base pairs. The strategy is simple. Base pairs are ``strongly encouraged'' to form by using large bonus energies. The default is -500, or -50 kcal/mole per forced base pair. The artificial energies are automatically subtracted from the energies printed in the output files, but the bonus energies do affect the dot plot and the automatic generation of structures in the ``N best'' mode. These effects are outlined in (6.2).

next up previous   Next: 4.2 The ``Single Up: 4. Methods 2 Previous: 4. Methods 2

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