Rule-based structure generation

Rule-based structure generation techniques, 16 751-752 Rule of 5, in diversity analysis, 6 18 Rules... 

In principle, two different classes of structure generators can be distinguished, namely empirical approaches,. such as fragment-based or rule- and data-based... 

A widely used 3D structure generator is CONCORD [131, 132] (for a more detailed description see Chapter II, Section 7.1 in the Handbook). CONCORD is also a rule- and data-based program system and uses a simplified force field for geometry optimization, CONCORD converts structures from 2D to 3D fairly fast... 

By now many sorts of reactive intermediates, such as free radicals, carbocations, carbenes, benzynes, and Bredt s rule violating olefins, have been generated and isolated under conditions permitting full structural characterizations. Theory-based structural parameters are generally in nearly perfect agreement with experimentally determined values. 

Expert systems have been defined as any formal systems , which make predictions about the toxicity of chemicals. All expert systems for the prediction of toxicity are built on experimental data and/or rules derived from such data (Dearden 2003). The expert systems can be further divided into two subclasses based on the method of generating rules. The one method is a knowledge- or rule-based expert system, for which experts/toxicologists create rules based on a list of structural features that have been related to a specified toxicity (Durham and Pearl 2001). An example of a typical knowledge- or rule-based system is DEREK, which will be described later. 

One of the primary issues with systematic nomenclature is that some names can appear systematic in nature but, in fact, are not. They can have the expected structure of a chemical name generated according to a rules-based system but are false systematic names, at least in their specific context. When the N2S conversion algorithms... 

DENDRAL uses a set of rule-based methods to deduce the molecular structure of organic chemical compounds from chemical analysis and mass-spectrometry data. This process includes detecting structural fragments, generating structural formula from these fragments, and verifying it by determining the correlation between... 

The ligand molecules are taken from a compound databases typically containing only structural formulae of the individual molecules. In order to use them in a docking calculation, 3D structures of the molecules have be generated. For this step, very powerful tools like Concord [166] or Corina [68, 69] exist. In addition, atom hybridization and protonation as well as bond types have to be determined. Typically, this task is performed by a series of subsequently executed rule-based scripts. It should be noted that due to the complexity of this task, the resulting structures are not free of errors in the assignment of atom and bond types. The docking software should therefore rely as little as possible on this information. 

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