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Molecular recognition between proteins and small-molecule metabolites plays a crucial role in regulating protein function and controlling various cellular processes. The activities of metabolic enzymes, transcription factors, transporters, and membrane receptors can all be mediated by protein-metabolite interactions (PMIs), thereby linking cellular metabolism with genetic/epigenetic regulation, environmental sensing, and signaling transduction. In addition to directly binding to the active or orthosteric sites of native cognate proteins, metabolites are also known to interact with different allosteric sites, allowing additional specific modulation of protein and macromolecular protein assembly structure and function. Metabolic protein interaction studies (PMIs), a method for assessing proteome binding with associated metabolites, can reveal novel allosteric and enzymatic functions, and can provide an excellent study for studying drug targets in the native cellular context tool.