Rules

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Revision as of 09:36, 7 December 2020 by Schmid (talk | contribs) (Reaction Patterns - SMIRKS)
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In enviPath, a rule object represents a biotransformation rule. Biotransformation rules are generalizations of reactions and used for the prediction of pathways. The left-hand side of a rule represents a pattern that matches functional groups in compounds. If the functional group is matched, a transformation described via a mapping to the right-hand side of the rule is carried out.

Available Rules

A list of all available rules is provided here. To view all rules of a particular package, select the package first, then the rules within his package (http://evipath.org/package/<id>/rule).

Description

The description explains the general biochemical reaction represented by a given rule and also explains any exceptions (e.g., substructures that prevent application of the rule).

Reaction Patterns - SMIRKS

A rule consists of one (simple rule) or several (composite rule) reaction patterns. Each pattern is represented by a SMIRKS string. enviPath can import or export transformation rules using this format. Additionally, the web interface offers the graphical molecule editor Ketcher, which can create transformation rules that can be stored directly from the editor.

EC numbers

Here, 4th level EC (Enzyme Commission) numbers (see numerical classification scheme for enzymes recommended by IUBMB) are listed for enzymes known to catalyze reactions that are consistent with the respective rule. Details on how these rule-enzymes linkages were generated are described in Schmid, Fenner, enviLink: A database linking contaminant biotransformation rules to enzyme classes in support of functional association mining, submitted to Biofinformatics, 2020.

Additional fields

  • A rule can have additional SMARTS filter that exclude matching products or reactants when applying the rule.
  • In the core data provided in enviPath, the aerobic rule likelihood is stored as additional information. This information can be used to apply a truncation strategy when predicting a pathway, e.g. to suppress reactions that are unlikely under aerobic conditions.