By Douglas H. Turner, David H. Mathews
This quantity presents protocols and strategies for deciding on and modeling RNA structure. Chapters consultant the reader via protocols for RNA secondary constitution prediction, unmarried series modeling, Crumple, RNAstructure to version conserved secondary buildings with a number of homologs, the prediction of bimolecular secondary constructions with RNAstructure, STarMir, protocols for constitution mapping, mapping facts to constrain or restrain RNA secondary constitution prediction with RNAstructure, unassigned NMR resonances, modeling protocols for Rosetta FARFAR, RNAComposer , ModeRNA, and MC-Fold. Written within the hugely profitable Methods in Molecular Biology series structure, chapters contain introductions to their respective themes, lists of the required fabrics and reagents, step by step, quite simply reproducible laboratory protocols, and tips about troubleshooting and keeping off identified pitfalls.
Authoritative and useful, RNA constitution selection: equipment and Protocols goals to make sure winning ends up in the additional research of this important field.
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Extra resources for RNA Structure Determination: Methods and Protocols
5. Pseudoknots are often not predicted, and the prediction accuracy is generally low if they are included. Methods such as the partition function calculation and energy dot plot can complement the free energy minimization method. It is also recommended that multiple methods are used depending on the situation. For example, Fold, energy dot plot, partition function, and stochastic sampling could be run on a riboswitch RNA  to develop hypotheses about its different conformations. If homologous sequences are available, prediction algorithms of multiple sequences, such as Multilign  and TurboFold , are more accurate.
These algorithms allow pseudoknots of more diverse topologies, but they do not guarantee the minimum free energy structure will be found. A third class of algorithms combines graph algorithms with dynamic programming algorithms for optimal pseudoknotted structure prediction to improve the computation efficiency [45, 46]. Although algorithms for pseudoknot prediction are now computationally tractable, it was shown that the accuracy of pseudoknot prediction is poor , suggesting the need for improvement.
The letter “X” is used to indicate unknown nucleotides that will not be allowed to pair. Lowercase letter(s) are used to force nucleotide(s) to be single-stranded in the prediction. Any number of white space characters is allowed in the sequences. 5. The sequence must end with “1”. ct extension. 8): 1. The first line must start with the sequence length, followed by the title of the structure. Each of the following lines provides the information on each nucleotide in the sequence. It must contain six fields separated by an arbitrary number of spaces: (1) nucleotide position i; (2) a single letter for nucleotide (A, U, T, G, C, or X) in either lower or upper case; (3) the preceding nucleotide to this nucleotide (position i-1 or 0 for the 5′ end); (4) the following nucleotide in the sequence (position i + 1 or 0 at the 3′ end); (5) position of the nucleotide to which this nucleotide is base paired, where no pairing is indicated by 0; (6) natural numbering, which is ignored by RNAstructure and usually set to repeat i.