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Fig. 6 | Journal of Cheminformatics

Fig. 6

From: Predicting the mutation effects of protein–ligand interactions via end-point binding free energy calculations: strategies and analyses

Fig. 6

Correlation between the predicted binding free energy difference and the experimental data of the D7R4-tryptamine systems in different MD simulation time, where the standard MM/GBSA results based on 20 and 100 ns MD simulation (εin = 1) are shown in panel A. The energetic difference of the vital residues between the D111L mutant and the wild-type system is shown in panel B with the corresponding most populated conformations illustrated in panel C, in which structures derived from 20 and 100 ns MD simulations are colored in blue and orange, respectively, with the mutation site colored in red

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