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Fig. 4 | BMC Genomics

Fig. 4

From: Protein targets of thiazolidinone derivatives in Toxoplasma gondii and insights into their binding to ROP18

Fig. 4

RMSD as a function of the simulation time. In panels (a) and (b), plots of the RMSD calculated with the α-carbons of the protein after aligning them to the initial structure with the Kabsch algorithm. In panels (c) and (d), plots of the RMSD calculated with all heavy atoms of the corresponding ligand, previously aligning the structures to the initial conformation with the mass weighted Kabsch. Each plot corresponds to one of the four MDs performed with each system. Plots corresponding to the TgROP18/ATP complex are colored in orange tones, panels (a) and (c), and the ones corresponding to TgROP/30C are colored in blue tones, panels (b) and (d). The red line at 100 ns indicates the time used for the beginning of the analysis, where the systems are considered equilibrated

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