ATLAS of Biochemistry

A repository of all possible biochemical reactions for synthetic biology and metabolic engineering studies. The database is free for academic use upon subscription.

TABLES

Curated KEGG reactions

  • 6’528 BNICE.ch-curated KEGG reactions
  • KEGG reactions are reconstructed in one, two or three reaction steps
  • Suggestions for EC classification up to the 3rd level EC number
  • Gibbs free energy estimated by Group Contribution Method (GCM)

ATLAS Reactions

  • 137’416 known and novel reactions generated by BNICE.ch
  • Suggestions for EC classification up to the 3rd level EC number
  • Structurally most similar KEGG reaction found by BridgIT, including a similarity score
  • Gibbs free energy estimated by Group Contribution Method (GCM)

TOOLS

Pathway search

Our database allows the user to search for all the possible routes from any substrate compound to any product. Resulting pathways involve known and novel enzymatic steps that may indicate unidentified enzymatic activities as well as providing potential targets for protein engineering to alter substrate specificity.
Example: Search for a pathway between two metabolites to bridge a gap in a metabolic model.

Reaction map

The reaction map finds all KEGG compounds connected to a given source compound in one, two or more reaction steps.
Example: Search the metabolic environment of a experimentally measured metabolite for pathways that connect the metabolite to the known metabolic network of the organism under study.