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The bi-directional selective low toxicity/high flame retardancy organophosphorus fire retardants (OPFRs) derivatives were designed by a comprehensive effect 3D quantitative structure-activity relationship (QSAR) pharmacophore model, and the toxicity and flame retardancy mechanism of OPFR derivatives were explored. The 3D-QSAR comprehensive pharmacophore model was constructed using the toxicity/flame retardancy comprehensive evaluation values of OPFRs for molecular modifications, which were obtained by the Mamdani fuzzy inference approach.