rules
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| ====== Rules ====== | ====== Rules ====== | ||
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| - | From enviPath Wiki | ||
| - | Jump to navigation Jump to search | ||
| 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. | 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. | ||
| - | ===== Contents ===== | ||
| + | ===== Available Rules ===== | ||
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| - | * 1 Available Rules | ||
| - | * 2 Description | ||
| - | * 3 Reaction Patterns - SMIRKS | ||
| - | * 4 EC numbers | ||
| - | * 5 Additional fields | ||
| - | + | A list of all available rules in enviPath can be found [[https:// | |
| - | ===== Available Rules ===== | + | |
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| - | 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:// | ||
| ===== Description ===== | ===== Description ===== | ||
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| - | 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, | + | A rule consists of one (simple rule) or several (composite rule) reaction patterns. Each pattern is represented by a [[https:// |
| ===== EC numbers ===== | ===== 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, | + | Here, 4th level EC (Enzyme Commission) numbers (see [[http:// |
| ===== Additional fields ===== | ===== Additional fields ===== | ||
| - | A rule can have additional SMARTS filter that exclude matching products or reactants when applying the rule. | + | * A rule can have additional |
| - | 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. | + | |
| - | Retrieved from " | + | |
rules.1700494702.txt.gz · Last modified: 2023/11/20 15:38 by shankar