| ## 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 RNA folding parameters is available at the NNDB. The latest complete set of rules based on experiments (and those used by RNAstructure) are the Turner 2004 rules. These are described in detail in: Mathews, D. H., Disney, M. D., Childs, J. L., Schroeder, S. J., Zuker, M. & Turner, D. H. (2004). Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proceedings of the National Academy of Sciences, USA. 101, 7287-7292. The enthalpy parameters, for extrapolating to temperatures other than 37 degrees C are described in: Lu, Z. J., Turner, D. H., & Mathews, D. H. (2006). A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation. Nucleic Acids Research. 34, 4912-4924. The Watson-Crick helix rules are provided by: Xia, T., SantaLucia, J., Jr., Burkard, M. E., Kierzek, R., Schroeder, S. J., Jiao, X., Cox, C. and Turner, D. H. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick pairs. Biochemistry, 37, 14719-14735. RNAstructure also comes with thermodynamic parameters for DNA and for an RNA alphabet with m6A, which includes A, C, G, U, and m6A. ### Where are the thermodynamic parameters located? The tables are located in the RNAstructure subdirectory data_tables/ . ### What do the files mean? The current tables are formatted in a format: alphabet.type.dg/dh/dat where the current alphabets are rna, dna, m6A, msa, or b-test. msa are the set of RNA parameters used by AlignmentFold and AlignmentPartion for multiple sequence alignments. b-test is an alphabet used for testing the extended alphabet, where B is a new nucleotide with folding thermodynamics identical to A. The .dg files are folding free energies at 37 degrees C and .dh is the folding enthalpy changes. Enthalpies are used for predicting secondary structures at temperatures other than 37 degrees C and are only available for rna, dna, and b-test. The *.specification.dat file is used to define the alphabet, including the allowed nucleotides and the possible base pairs. There are also a set of tables that are in the format: type.dat, type.dh, dnatype.dat, or dnatype.dh. These are the older parameter format and are still used by the GPU programs at compile time. Finally, some programs use additional data that are stored here: Fold can use a mapping data and a gamma function to estimate the logs odds of a nucleotide being paired vs. unpaired. The subdirectory dists hold the parameters for the gamma function. Rsample uses a set of reactivity distributions to interpret SHAPE data. These distributions are in the subdirectory rsample. multifind uses an SVM to classify alignments contents as conserved, structured ncRNA or not. The model for the SVM is in data_assemble_training_Multifind_predict_ensemble_z_final_svmformat.model design can use a set of loop and helix sequences that are predetermined to work well together. Those are in files name design.RNA/DNA.Helices/Loops.dat. OligoWalk uses helix.dat and helixdr.dat to store helix free enrgy change nearest neighbors for RNA-RNA and DNA-RNA, respectively. The DNA-RNA helix parameters are from: Sugimoto, N., Nakano, S., Katoh, M., Matsumura, A., Nakamuta, H., Ohmichi, T., Yoneyama, M., Sasaki, M. 1995. Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry. 34, 11211–11216. ### What does each table type contain? *.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. More about how the parameters are used and their values can be found in the NNDB.