Secondary-, structural notation

Inverse folding can be viewed as an optimization problem that can be treated with simple heuristics. This is what the RNAinverse program does for you. Input for the RNAinverse program consists of an RNA secondary structure (the target) in bracket notation (on the first line), optionally followed by a sequence to be used as the starting point of the optimization (otherwise a random start sequence is used). 

Fig. 2.7. RNA secondary structures. The nucleotide sequence oftRNAphe (shown in the upper string) is presented together with the secondary structure of minimal free energy and the symbolic notation (lower string). The sequence contains several modified nucleotides (D, M, P, T, Y) in addition to the conventional bases (A, U, C, C). Individual nucleotides in the secondary structure are shown as light gray (single bases), dark gray and black pearls (base pairs). ThetRNA structure is a clover leaf with three hairpin loops (adjacent stacks are shown in black) and a closing stack...

In the lower part of the RNAz output the predicted structures are explicitly seen for the sequences. There will be structure predictions for each single sequence and a consensus structure prediction for the whole alignment. The predicted structures are given below the sequences in a dot-bracket notation. Each basepair in the secondary structure is indicated by a pair of brackets ( and ) . Unpaired bases are shown as dot Next to the structure the... 

The output contains a consensus sequence and the consensus structure in bracket notation. The bracket notation is convenient string representation for secondary structures. It encodes the structure as a string of dots and matching... 

Figure 2.10 Secondary and tertiary structure of the enzyme lysozyme, PDB 2C80. Visualized using Cambridge Soft Chem3D Ultra 10.0 with notations in ChemDraw Ultra 10.0. ChemDraw Ultra, version 10.0. (Printed with permission of CambridgeSoft...

Figure 7.2 The structure of the faster reacting enantiomer in lipase-catalyzed esterification in kinetic resolution of racemic secondary alcohols or hydrolysis of the corresponding esters. Small and large refer to the relative size of the groups and not to the R/S notation.

The tricarboxylate cycle is marked parts of the products are obviated into both metal mobriization and amino acid synthesis (over a couple of intermediates). Neither structures nor chemical classification of secondary chelators in the (larger, upper) roots or shoot are known in general (Clemens et al. 2002). Like commonplace in chemical notation, catalyst ions (metals which become active in metaUoproteins) are denoted by swift brackets M disregarding issues tike speciation or oxidation state (which may periodically change in a catalytic cycle anyway) whereas complexes are shown in square brackets. To yet allow for effective growth, the investment of organics to obtain metal ions from soil must be kept as small as possible... 

Generally, the solids are not structurally homogeneous, but the solid and liquid nevertheless will be called phases and leaching will be treated as a two-phase, mass transfer process- The solid consists of a matrix of insoluble solids, the mare, and the occluded solution. It may also contain undissolved solute and a nonextractable secondary phase, for example, coffee oil in water-soaked coffee grounds. This secondary phase is treated as part of the mate. Dimensionless parameters that can affect solnta transfer include the solute equilibrium distribution coefficients, m and M tha Pick number, v the strippirg factor, a the Biot number, Bi and the Peclet number, Be. These parameters are defined more precisely in the Notation section. 

Figure 6.2 A SMARTS notation to specify a primary or secondary amine that is not an amide. This substructure pattern will match the shaded nitrogen atoms in the structure diagram, but not the unshaded one.

As with the numeric data, the content of stmctural information in the secondary literature is fimited, and we therefore have a situation in which many specicdised systems have been developed to deal with stractural data. Files of chemical stractures, and means of accessing them, have been with us for a number of years, certainly from before computers. Traditionally, these have used notations, fragment codes, etc., as the means of recording structural information, and have allowed searches to be made for complete compounds or for all compounds containing certain specified substractures. More recently, topographical systems have been developed. In these the complete stractures are recorded in the form of "connection tables", which store full details of all the atoms and bonds in a molecule, and the precise arrangement in which they are connected. 

---