Object[Simulation, Folding]
A simulation to predict the secondary structure of a given nucleic acid oligomer by considering the formation of potential intramolecular Watson-Crick pairing between nucleotides.
Organizational Information
Name
Name of this Object.
Format: Single
Class: String
Programmatic Pattern: _String
Pattern Description: A string.
ID
ID of this Object.
Format: Single
Class: String
Programmatic Pattern: _String
Pattern Description: The ID of this object.
Object
Object of this Object.
Format: Single
Class: Expression
Programmatic Pattern: Object[Simulation, Folding, _String]
Pattern Description: The object reference of this object.
Type
Type of this Object.
Format: Single
Class: Expression
Programmatic Pattern: Object[Simulation, Folding]
Pattern Description: Object[Simulation, Folding]
Notebook
Notebook this object belongs to.
Format: Single
Class: Link
Programmatic Pattern: _Link
Pattern Description: An object of that matches ObjectP[Object[LaboratoryNotebook]].
Relation: Object[LaboratoryNotebook][Objects]
Status
The current status of the simulation.
Format: Single
Class: Expression
Programmatic Pattern: ProtocolStatusP
Author
The person who requested this simulation.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[User][SimulationsAuthored]
DateConfirmed
The date on which the simulation first entered processing or a backlog.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
DateEnqueued
The date on which the simulation first entered processing or a backlog.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
DateStarted
Date when this simulation was started.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
DateCompleted
Date when this simulation was completed.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
DateCanceled
Date when this simulation was canceled.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
TimeElapsed
The time that was required to complete the simulation.
Format: Computable
Programmatic Pattern: GreaterEqualP[0 Day]
Expression: SafeEvaluate[{Field[DateCompleted], Field[DateStarted]}, Computables`Private`timeElapsed[Field[DateCompleted], Field[DateStarted]]]
Option Handling
UnresolvedOptions
The unresolved options entered into the simulation function that generated this object.
Format: Single
Class: Compressed
Programmatic Pattern: {_Rule...}
ResolvedOptions
The options resolved automatically by this simulation or entered by the requestor.
Format: Single
Class: Compressed
Programmatic Pattern: {_Rule...}
General
StartingMaterial
The objects containing the source structure used in this simulation.
Format: Single
Class: Link
Programmatic Pattern: _Link
InitialStructure
The starting structure of the nucleic acid oligomer which will be used as a template to add additional foldings to.
Format: Single
Class: Expression
Programmatic Pattern: StructureP
Method
The type of algorithm used to predict the folding of the macromolecule.
Format: Single
Class: Expression
Programmatic Pattern: FoldingSimulationMethodP
Heuristic
Indicates if the algoritm optimizes for the maximum number of bonds in the structures or the minimal energy of the structures.
Format: Single
Class: Expression
Programmatic Pattern: HybridizationMethodP
FoldingInterval
The interval of the given starting structure over which folds will be computed.
Format: Single
[[1]] Strand Index
Header: Strand Index
Class: Integer
Programmatic Pattern: GreaterP[0, 1]
[[2]] Starting Base Number
Header: Starting Base Number
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterP[0 Nucleotide, 1 Nucleotide]
[[3]] Ending Base Number
Header: Ending Base Number
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterP[0 Nucleotide, 1 Nucleotide]
Temperature
Temperature at which Gibbs free energy of folded structure will be calculated.
Format: Single
Class: Real
Unit: 1 degree Celsius
Programmatic Pattern: GreaterP[0 Kelvin]
Depth
Number of iterative folding steps conducted by the folding algorithm to reach the final structures.
Format: Single
Class: Expression
Programmatic Pattern: GreaterEqualP[1, 1] | {GreaterEqualP[1, 1]} | Infinity
Breadth
Number of candidate structures to propagate forward at each iterative step in the folding algorithm.
Format: Single
Class: Expression
Programmatic Pattern: GreaterEqualP[1, 1] | Infinity
Consolidate
Indicates if all folds are extended to their maximum length.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
SubOptimalStructureTolerance
Threshold below which suboptimal structures will not be considered. If specified as integer, results will include all structures within the provided number of the optimal folded structure's bond count. If specified as energy, results will include all structures whose energy is within the provided absolute energy of the optimal folded structure's energy. If specified as percent, result will include all structures whose energy is within the provided percent of the optimal folded structure's energy.
Format: Single
Class: Expression
Programmatic Pattern: GreaterEqualP[0, 1] | GreaterEqualP[0 percent] | GreaterEqualP[0 thermochemical kilocalories per mole]
MinLevel
Minimum number of bases required in each fold.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
MaxMismatch
Maximum number of mismatches allowed in each folded duplex.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
MinPieceSize
Minimum number of consecutive paired bases required in a fold containing mismatches.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
ExcludedSubstructures
Types of substructures that are not considered by the folding algorithm.
Format: Multiple
Class: Expression
Programmatic Pattern: LoopTypeP
MinHairpinLoopSize
Lower bound (inclusive) on the allowed number of unpaired bases in a hairpin.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
MaxHairpinLoopSize
Upper bound (inclusive) on the allowed number of unpaired bases in a hairpin.
Format: Single
Class: Expression
Programmatic Pattern: GreaterEqualP[0, 1] | Infinity
MinInternalLoopSize
Lower bound (inclusive) on the allowed number of unpaired bases in an interior loop.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[2, 1]
MaxInternalLoopSize
Upper bound (inclusive) on the allowed number of unpaired bases in an interior loop.
Format: Single
Class: Expression
Programmatic Pattern: GreaterEqualP[2, 1] | Infinity
MinBulgeLoopSize
Lower bound (inclusive) on the allowed number of unpaired bases in a bulge loop.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[1, 1]
MaxBulgeLoopSize
Upper bound (inclusive) on the allowed number of unpaired bases in a bulge loop.
Format: Single
Class: Expression
Programmatic Pattern: GreaterEqualP[1, 1] | Infinity
MinMultipleLoopSize
Lower bound (inclusive) on the allowed number of unpaired bases between each paired section in a multi loop.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
Simulation Results
FoldedStructures
The final folded structures resulting from the simulation starting from the initial structure.
Format: Multiple
Class: Expression
Programmatic Pattern: StructureP
FoldedEnergies
For each member of FoldedStructures, the free energy of folding starting from the initial structure to the folded structure.
Format: Multiple
Class: Real
Unit: 1 thermochemical kilocalorie per mole
Programmatic Pattern: EnergyP
FoldedNumberOfBonds
For each member of FoldedStructures, the number of bonds in the folded structure.
Format: Multiple
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
FoldedPercentage
For each member of FoldedStructures, the percent composition of the folded structure at equilibrium.
Format: Multiple
Class: Real
Unit: 1 percent
Programmatic Pattern: GreaterEqualP[0 Percent]
Foldings
A table of the resulting folded structures, along with their energies, number of bonds, and precentage composition at equilibrium.
Format: Computable
Programmatic Pattern: FoldingsP
Expression: SafeEvaluate[{Field[FoldedStructures], Field[FoldedEnergies], Field[FoldedNumberOfBonds], Field[FoldedPercentage]}, Simulation`Private`foldsTranspose[{Field[FoldedStructures], Field[FoldedEnergies], Field[FoldedNumberOfBonds], Field[FoldedPercentage]}]]
Last modified on Mon 26 Sep 2022 15:43:53