RetroRules
RetroRules is a database of reaction rules for metabolic pathway discovery and metabolic engineering. RetroRules provides a complete set of reaction rules, extracted from public databases and expressed in the community-standard SMARTS format, augmented by a rule representation at different levels of specificity (the atomic environment around the reaction center). Such multiple representation of reactions expands natural chemical diversity by predicting de novo reactions of promiscuous enzymes. Our rules are readily usable by open source cheminformatics tools such as RDKit as well as more complex retrosynthetic codes such as RetroPath2.0.
Description
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RetroRules is a database of reaction rules for metabolic pathway discovery and metabolic engineering. RetroRules provides a complete set of reaction rules, extracted from public databases and expressed in the community-standard SMARTS format, augmented by a rule representation at different levels of specificity (the atomic environment around the reaction center). Such multiple representation of reactions expands natural chemical diversity by predicting de novo reactions of promiscuous enzymes. Our rules are readily usable by open source cheminformatics tools such as RDKit as well as more complex retrosynthetic codes such as RetroPath2.0.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:59.724807
Webpage:
https://retrorules.orgWebpage
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Licence:
Name: CC-BY-4.0Licence name
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Publications:
Publications
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RetroRules: a database of reaction rules for engineering biology
PMID: 30321422
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:59.724807
Publications
More detailed information about this field from each metasource.
RetroRules: a database of reaction rules for engineering biology
PMID: 30321422
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:59.724807
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RetroRules: a database of reaction rules for engineering biology
PubMed citations: 14.
14 articles citing: RetroRules: a database of reaction rules for engineering biology
Research progress of pathway and genome evolution in microbes. PMID:35224232
Biocatalysed synthesis planning using data-driven learning. PMID:35181654
Rhea, the reaction knowledgebase in 2022. PMID:34755880
EHreact: Extended Hasse Diagrams for the Extraction and Scoring of Enzymatic Reaction Templates. PMID:34587449
dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design. PMID:34570771
An extended reconstruction of human gut microbiota metabolism of dietary compounds. PMID:34354065
Evaluation of Heterologous Biosynthetic Pathways for Methanol-Based 5-Aminovalerate Production by Thermophilic Bacillus methanolicus. PMID:34262896
Metabolic engineering of Escherichia coli for de novo production of 3-phenylpropanol via retrobiosynthesis approach. PMID:34176467
RetroBioCat as a computer-aided synthesis planning tool for biocatalytic reactions and cascades. PMID:33604511
In silico design and automated learning to boost next-generation smart biomanufacturing. PMID:33344778
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models. PMID:33156326
Enzyme annotation in UniProtKB using Rhea. PMID:31688925
Metabolic perceptrons for neural computing in biological systems. PMID:31462649
The human gut chemical landscape predicts microbe-mediated biotransformation of foods and drugs. PMID:31184303
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bioengineering
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:59.724807
synthetic biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:59.724807
cheminformatics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:59.724807
molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:59.724807
Tags
More detailed information about this field from each metasource.
bioengineering
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:59.724807
synthetic biology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:59.724807
cheminformatics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:59.724807
molecular interactions, pathways and networks
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:59.724807
bioengineering synthetic biology cheminformatics molecular interactions, pathways and networks
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