Water pollution, particularly from industrial contaminants such as dyes, is a significant global concern. Various technologies, including nanoscale materials, are employed for water and wastewater treatment. Among these, adsorption process as an effective method due to its simplicity, cost-effectiveness, and reliability. This study comprised both theoretical and experimental phases. Initially, computer simulations were utilized to evaluate the interaction between methylene blue and three selected nanoparticles, ultimately choosing Bovine Serum Albumin protein nanoadsorbent based on energy considerations. Subsequently, adsorption experiments were conducted using this nanosorbent. The results indicated a maximum dye removal efficiency of 69% under the conditions of pH 11, an initial dye concentration of 100 mg/L, an adsorbent dose of 0.5 g/L, a contact time of 60 min, and an optimal temperature of 25 °C. The maximum adsorption capacity under optimal conditions was found to be 38.52 mg/g. Additionally, the adsorption isotherm followed the Langmuir equation, and the kinetics adhered to the pseudo-second-order model.