ThermodynamicParameters

Thermodynamic Parameter Tables

What are thermodynamic parameters?

We can use a set of nearest neighbor parameters to estimate the folding stability of structures. For RNA, these are called Turner rules.

A tutorial for understanding and using these parameters is available at the NNDB. The latest set of rules (and those used by RNAstructure) are the Turner 2004 rules.

Where are the thermodynamic parameters located?

The tables are located in the GTFoldPython subdirectory Python/Testing/ExtraGTFoldThermoData. See also the gtDMMB project GTModify for information on how to modify and prepare these sets of thermodynamic parameter data for use with GTFold.

What does each table contain?

The tables are formatted starting with the nucleotide/alphabet type. rna predes the RNA tables. dna precedes the DNA tables. b-test precedes a set of test tables for RNA that include a 'B' nucleotide that is the same as 'A'. These are used to test the code to ensure the alphabet works beyond A, C, G, and U/T.

The suffix indicates the type of parameter. dg are free energy change at 37 degrees C parameters and dh are enthalpy change parameters. dat is used for tables that specify the alphabet information. See the file-by-file specification for the custom energy models.

Note that for many terminal stack tables, the AU/GU helix end penalty is included for computational speed.