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The use of antibiotics has increased significantly recently. Humans and animals are unable to metabolize antibiotics completely. So, these antibiotics are released into the aquatic environments. Different blue-green and green algae are the major non-target organisms affected by antibiotics except bacteria. This study showed that antibiotics inhibit different proteins that are required for photosynthesis. Data showed that gentamicin, ampicillin, chloramphenicol, erythromycin, and rifamycin majorly affected the PSI proteins, whereas iclaprim, clindamycin, sulfadiazine, and tetracycline affected the PSII proteins. Two antibiotics, viz., ciprofloxacin, and nalidixic acid targeted cytochrome (cyt b6f). Results proved that rifamycin, erythromycin, and tetracycline were highly toxic with the lowest binding energies of −12.22, −12.13, and −10.45 kcal/mol. LigPlot + software revealed the binding site of the proteins for the …