The development of new pesticides as well as new approaches in their application are important challenges for food security. Currently, bioinformatics methods are useful for searching and designing models of molecular target structures, including antiviral, fungicidal, bactericidal, insecticidal, herbicidal drugs and plant growth regulators, which have been recently used in agrochemical research. In this article, we present the findings of a study investigating the molecular mechanisms underlying the binding of fungicides (fluopicolide, propamocarb) to target proteins (cytochrome P450, glutathione-S-transferases) of Phytophthora infestans. Virtual three-dimensional complexes of pesticides and their targets have been created using bioinformatics methods. A new approach for identifying the cavity parameters of binding sites using machine learning technology has been proposed. Rigid docking of pesticides with targets has been carried out and the binding energy calculation showed a high degree of stability of ligand-protein complexes. Our proposed in silico approach may be useful for studying the molecular mechanisms of fungicides action on Phytophthora proteins.