SMIRKS reaction SMILES

Reaction SMILES represents a specific reaction between specific reactants yielding specific products. As such, it can be very useful to store a library of reactions of interest. These might be a record of reactions that have been carried out at a company, a set of reaction plans in an academic research group, or even a set of hypothetical reactions that might never succeed in the laboratory. There is another extension of SMILES called SMIRKS that is more general and can represent a class of reactions. 

The word reaction is typically used to represent a specific reaction as well as a general transformation. In this chapter, the word reaction is used to mean a specific reaction represented using reaction SMILES. The word transformation is used to indicate a change in a set of reactants to products. SMIRKS is the language used to specify precisely how this transformation is to be carried out. 

Simplified Molecular-Input Line-Entiy System (SMILES) that are used to represent chemical reactions digitally are called reaction SMILES. SMIRKS [32] is a Itybrid... 

Other related coding languages are derived from enhancements of SMILES (XSMILES, SMARTS, SMIRKS, STRAPS, CHUCKLES, CHORTLES, CHARTS [22]). Each of them was designed to represent special molecular structures or to allow particular applications (polymers, mixtures, reactions, or database-handling). 

Daylight has extended SMILES rules to accommodate general descriptions of molecular patterns and chemical reactions (13). These SMILES extensions are called SMARTS and SMIRKS. SMARTS is a language for describing molecular patterns while SMIRKS defines rules for chemical reaction transformations. 

The binding calculator computes the feasibility of a particular vMol binding to a vEnz, based on quantitative structure-activity relationships (or decision tree) derived from properties of known substrates for each enzyme. Transformations are stored as a list of SMIRKS (SMILES Reaction Specification)... 

The use of Simplified Molecular Input Line Entry System (SMILES) as a string representation of chemical structure makes possible much of what has been discussed in earlier chapters of this book. A chemical reaction could be represented as a collection of SMILES, some identified as reactants and some as products. It is possible to define a table to do this, or perhaps use some arrays of character data types, but a syntax extension of standard SMILES allows reaction to be expressed easily. SMIRKS is an extension of SMILES and SMiles ARbitrary Target Specification (SMARTS). It is used to represent chemical transformations. SMIRKS can also be used in a transformation function to combine SMILES reactants to produce SMILES products. 

SMILES - simplified molecular line entry specification. A very terse linear notation which is much easier to create and to decode than the notorious WLN (Wiswesser line notation). Variations of SMILES include SSMILES, USMILES, SMARTS, SMIRKS, STRAPS, GHUGKLES, GHORTLES, and GHARTS which add features such as substructure search operators, reactions, combinatorial chemistry, and unique naming. ... 

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