<p>The aim of this work was to analyze the interactions of methyl-β-cyclodextrin and amphotericin B (AmB) with spectrin, actin, and hemoglobin by the method of molecular docking. The protein structures were taken from PDB. The full-atom models of proteins were “cleaned” of water molecules and buffer components, surface charge arrangement was performed, and cells were selected for “blind” docking. The structural formulas of methyl-β-cyclodextrin and amphotericin B were taken from PubChem and converted to HyperChem. Geometrical optimization was performed using the MM+ model potential; rigid/fixed structures were optimized using the PM3 semi-empirical quantum chemical method. The protein–ligand complex interactions were described using PLIP. The total binding energy for all complexes ranged from –4.4 to –10.3 kcal/mol. The complexes were formed due to hydrogen and van der Waals bonds and salt bridges. Visualization of the most energetically advantageous positions confirmed that both amphotericin B and methyl-β-cyclodextrin were located in the central cavities of hemoglobin and actin and in the distal sites of the α- and β-subunits of spectrin. Amphotericin B formed more stable complexes with each of the proteins: the strength of hydrogen bonds and the number of hydrophobic contacts with the proteins were higher than for complexes with methyl-β-cyclodextrin.</p>