Options from a bonds will be created between strands that are not connected:

If two strands are already connected by bonds, then inter-strand bonds can be created:

Kinetic folding method can return pseudoknots, which are excluded by the thermodynamic folding algorithm:

Long strands can be folded into a variety of structures with and without pseudoknots:

Using AlternativeParameterization to provide the thermodynamic parameters or to override the values taken from Thermodynamics field in the model oligomer:

Specify the number of folds to propagate forward at each level of the folding tree:

Specify Consilidate to be False to return subfolds:

Specify number of times to fold the input sequence:

When you exclude no substructures (all are allowed):

By excluding internal loops (this includes mismatches), we get the most optimal structure that does not have internal loops:

By excluding bulge loops and internal loops, we get the new most optimal structure (no bulge/internal loops) and a structure whose energy is within 25% of the optimal structure's energy:

For sequences, specify interval as list of positions in the sequence:

For strands, specify interval as motif position and sequence positions:

For structures, specify interval as Strand position, motif position, and sequence positions:

By default, thermodynamic folding attempts to optimize the energy of the folded structure (i.e. best structure has lowest Gibbs Free Energy):

When you allow any bulge loop size in the folded structure, a bulge loop of size 5 appears:

But by only allowing bulges where the bulge is 3 bases or smaller, the above result will be excluded, and the next-most optimal result (a structure with an internal loop) will be returned instead:

When you allow any hairpin loop size in the folded structure, a hairpin loop of size 6 appears:

But by only allowing hairpins where the number of loop bases is 3 or fewer, the above result will be excluded, and hairpin loop of size 3 appears:

When you allow any internal loop size in the folded structure, an internal loop of size 8 appears:

But by only allow internal loops where the size is 3 bases or smaller, the above result will be excluded, and the next-most optimal result will be returned:

When you do not allow mismatch, sequence "CCCACCAAAGG" can not return a valid folded structure:

But by allowing mismatches of size 1, two structures with a bulge loop appears:

Thermodynamic method uses planar folding algorithm which misses pseudoknots:

Kinetic method can return structures with pseudoknots which cannot be found by Thermodynamic method:

When you allow the lowest minimum bulge loop size, a bulge loop of size 1 appears:

But by only allowing bulges larger than 1 base (so no single-base bulges allowed), the above result will be excluded and the next-most optimal result (a structure with a single mismatch) will be returned::

When you allow any hairpin loop size in the folded structure:

But by only allowing hairpins that are 6 bases or larger, the above result will be excluded, and a hairpin loop of size 6 appears:

When you allow the lowest minimum internal loop size, an internal loop of size 2 appears:

But by only allowing internal loops of size 4 or greater. The smaller internal loop gets absorbed into the hairpin while the bigger internal loop stays:

Specify minimum number of bases required in each fold:

When you allow all multiple loops:

But by only allowing multiple loops with at least one free base between each 'branch', the next most optimal structure satisfying this condition does not have a multiple loop:

Specify minimum number of consecutive paired bases required in a fold containing mismatches:

When the input sequence is ambiguous, Polymer is defaulted to DNA:

But you can use Polymer option to specify the sequence to be RNA:

SubOptimalStructureTolerance is usally set to 25. Here, we use an energy value as tolerance:

When you allow 0 tolerance (only the optimal structure is returned):

You can use a bond-count tolerance to return all structures within a certain number of the optimal folded structure's bond count:

Use a percentage tolerance:

Specify temperature at which folding is simulated:

The options from a previous folding simulation can be used to create new foldings (object reference):

The options from a previous folding simulation can be used to create new foldings (object):

Using ThermodynamicsModel to explicitly provide the thermodynamic parameters or to override the values taken from Thermodynamics field in the model oligomer:

Maps over input:

Invalid sequence will fail:

Invalid strand will fail:

Invalid structure will fail:

Mix polymer type is currently unsupported:

Structure with unbounded strand will not be folded: