Overview
BAM generates and ranks structural candidates for suspect metabolites by applying biotransformation rules to known anchor structures. It combines reaction-derived operators and site-of-metabolism prediction with anchor-suspect relationships from molecular networks.
What can this tool do?
Common uses
- BAM generates and ranks structural candidates for suspect metabolites by applying biotransformation rules to known anchor structures.
Scientific fit
Primary function
Metabolite annotation and identification
Other functions
Molecular networking and chemical similarity
Analysis types
Untargeted metabolomics
Data compatibility
Inputs
Compound list or annotations, Molecular structures
Outputs
Molecular structures, Statistical results
Input formats
Reaction/metabolite CSV data and mass/SMILES anchor-suspect pairs
Output formats
Generated and ranked candidate structures with evaluation artifacts
Scope and considerations
Designed for
- BAM generates and ranks structural candidates for suspect metabolites by applying biotransformation rules to known anchor structures.
Not designed for
- Raw spectral network construction or confirmed structural identification without validating the generated candidate and proposed transformation.
Important requirements
- Separate PROXIMAL2 and GNN-SOM installations/environments, configured reaction/metabolite CSV tables and anchor-suspect pairs containing masses and known anchor SMILES.
Considerations
- Reaction coverage, anchor correctness and site-of-metabolism predictions constrain candidate generation. KEGG and RetroRules examples retain their own data terms.
Access and documentation
Public research code; no repository-wide license grant was established. PROXIMAL2, GNN-SOM and reaction databases require separate installation and terms review.
Evidence and review
Enveda intake rechecked against official repository documentation, package/license metadata and primary publication identity on 2026-10-27. Editorial source review only; no software execution or independent benchmark. See docs/enveda-expansion-review-2026-10-27-batch3.md.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Molecular Structure Discovery for Untargeted Metabolomics Using Biotransformation Rules and Global Molecular Networking. Analytical Chemistry (2025). doi:10.1021/acs.analchem.4c01565
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-10-27 · First committed entry
Add 45 source-reviewed Enveda tool entries in third expansion batch
View change · Entry at this revision