PathDB
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- Web / downloadable Java system
General metabolic pathway database project at NCGR.
Compounds, reactions, enzymes and other metabolic proteins and pathways. Descriptions of kinetic, thermodynamic and physico-chemical properties of pathway components.
Pathway discovery tools: deal with arbitrary metabolic networks:
- Structural/ stoichiometric analysis - algorithms for automatic identification of mass conservation relations, routes between two arbitrary metabolites elementary flux modes
- Simulation of dynamics and control - Gepasi metabolic simulator
Visualization: automatic pathway layout program - user can visually inspect a set of reactions obtained from any query. Can be permanently stored pathways or routes between metabolites.