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Methods for investigations of <> relationships for conformational flexible molecules have been described. By means of exhaustive conformational search the methods allow one to find: the active chemicals for a specific biological interaction, the similarity between 3D structures of molecules and common reactivity patterns. The OASIS-COREPA approach accounting for conformational flexibility of chemicals has been employed for modeling of reintegration of the retinal derivatives into bacterioopsin in order to find the common structural requirements of protein molecule to retinoids’ molecules. The common reactivity pattern conditioning the high biological activity has been elucidated. The results are mechanistically reasonable confirming the hypothesis for two-stage process of reintegration and allowing prediction of novel and biologically active derivatives.