Structure generation rule-based methods

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... 

Molecular docking and structural alignment methods are based on three-dimensional structures of candidate molecules that can be generated by rule-based methods such as CORINA [13, 14] or CONCORD [15]. However, methods based on three-dimensional structures are computationally quite demanding and cannot routinely be applied to databases of hundreds of thousands of compounds today. For this reason, a number of fast methods to determine molecular similarity have been developed that operate solely on connectivity and atom types of molecules. Such tools allow rapid prescreening of very large databases and avoid a conformational analysis of each candidate molecule. 

OMEGA is a fast rule-based method and generates the conformation in a systematic manner [74]. It cuts a structure into several torsional fragments and reconstructs the molecule according to different rules with varying torsion angles. Finally, duplicate conformations (which have an RMS rz deviation less than or equal to 0.8 A)... 

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. 

Distinct from these are automatic methods that directly transform 2D input information on atoms, bonds, and stereochemistry into 3D atomic coordinates. The automatic methods are classified into rule-based and data-based, fragment-based, conformational analysis, and numerical methods (Fig. 5). These classes of methods overlap more or less with each other and belong more or less to the domain of automatic 3D structure generation ... 

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