PSAMM

PSAMM provides computational methods for curating, analyzing, and simulating metabolic models and infers element-transferring reactant/product pairs to clarify primary metabolite connectivity in metabolic networks.

Key Features:

• Metabolic model curation and management: Version tracking, structured annotations, data integration, and parsing/formatting of metabolic models.
• Quality control: Consistency checking to identify common issues in reaction and metabolite definitions.
• Model completion support: Automatic gap filling to reconcile missing links in reconstructed networks.
• Simulation workflows: Execution of simulation analyses on curated metabolic models.
• Element-transfer prediction: Algorithm to infer element-transferring reactant/product pairs to identify primary compound-to-compound connections.

Scientific Applications:

• Metabolic network reconstruction and curation: Assisting reconstruction and refinement of metabolic network models from reaction databases and genome-scale reconstructions.
• Pathway interpretation and network visualization: Clarifying primary reactant/product connections to improve pathway structure interpretation and network visualization.
• Systems biology and metabolic engineering analyses: Supporting analyses and hypothesis generation about metabolic organization and biochemical transformations.

Methodology:

PSAMM combines model management utilities (version tracking, annotation, parsing/formatting, and consistency checking) with analytical functions (automatic gap filling and simulation workflows); its element-transfer prediction infers likely element-transferring reactant/product pairs using information present in metabolic model representations and has been benchmarked against curated references.