Furnishes a collection of stereochemistry-aware reaction rules for engineering biology. RetroRules includes multiple data sources and automates the generation of ranked rules with variable specificity to reactants. It covers over 16 000 biochemical transformations, extracted from public databases. This repository can serve for the reproducibility for both protocols of experimental data analysis and in silico screening.
Reflects and summarizes peculiarities of Caenorhabditis elegans metabolism distinct from most other higher eukaryotes. ElegCyc is an online resource for data integration in context of metabolism as well as functional annotation of the metabolic network for the C. elegans community. This database brings along utilities for the analysis and visualization of large-scale datasets provided by Pathway Tools Omics Viewer.
Allows preliminary identification of metabolites using two properties. MMD is an online resource storing data from genome scale metabolic reconstructions, HMDB, KEGG, Lipid Maps, BioCyc and DrugBank. It supplies information on more than 42000 endogenous and exogenous metabolite species.
Allows users to study two contemporary organisms, T. maritima and E. coli. GEM-PRO maps genes in a metabolic model to their respective high-quality structural data. The repository connects the metabolic reconstruction together with protein-related data, such as experimental protein structures, complex stoichiometry, protein fold family and domain architecture. It assists researchers to formulate hypotheses about which proteins are most likely to act promiscuously on substrates other than their native one.
Consists of a genome-scale metabolic model for Methylococcus capsulatus. iMcBath represents a solution for hypothesis-driven metabolic identification. It can assist users in the curation process and furnishes annotations. This database is composed of more than 800 enzymatic reactions that interconvert over 780 unique metabolites. It integrates MIRIAM-compliant annotations for a majority of the model’s reactions and metabolites.
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