| ## RNAstructure Installation and Overview Thermodynamic Parameter Tables | ### Contents ### Index
## Thermodynamic Parameter Tables ### What are thermodynamic parameters? RNAstructure uses 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 RNAstructure subdirectory data_tables/ . ### 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. *.specification.dat indicates the alphabet and pairs. *.coaxial.* are parameters for flush coaxial stacking where two helix ends stack without an intervening mismatch. *.coaxstack.* are parameters for coaxial stacking of helices with an intervening mismatch. This is for the stack where the backbone is not continuous. *.dangle.* are parameters for dangling ends on pairs. *.hexaloop.* are parameters for hairpin loops of 6 unpaired nucleotides that have stabilities not well modeled by the parameters. *.int11.* are parameters for 1×1 internal loops. *.int21.* are parameters for 2×1 internal loops. *.int22.* are parameters for 2×2 internal loops. *.loop.* are parameters for loop initiations. *.misloop.* are parameters that do not fit into other tables. *.stack.* are parameters for helical stacking. *.tloop.* are parameters for hairpin loops of 4 unpaired nucleotides that have stabilities not well modeled by the parameters. *.triloop.* are parameters for hairpin loops of 3 unpaired nucleotides that have stabilities not well modeled by the parameters. *.tstack.* are parameters for terminal mismatches in exterior loops. *.tstackcoax.* are parameters for coaxial stacking of helices with an intervening mismatch. This is for the stack where the backbone is continuous. *.tstackh.* are parameters for first mismtaches in hairpin loops. *.tstacki.* are parameters for the mismatches in internal loops. *.tstacki23.* are parameters for the mismatches in 2×3 internal loops. *.tstackm.* are parameters for the mismatches in multibranch loops. Note that for many terminal stack tables, the AU/GU helix end penalty is included for computational speed.