Fig. 4: Comparisons of RMSF obtained from MD simulations with ligands, without ligands, and RMSF-net on ligand-containing protein systems. | Nature Communications

Fig. 4: Comparisons of RMSF obtained from MD simulations with ligands, without ligands, and RMSF-net on ligand-containing protein systems.

From: Accurate Prediction of Protein Structural Flexibility by Deep Learning Integrating Intricate Atomic Structures and Cryo-EM Density Information

Fig. 4

a Results for 6CM9. The top panel shows scatter plots of RMSF on residues, with colors corresponding to the three approaches as indicated in the legend. The middle panels present the visualizations of RMSF from the three approaches on the PDB structure, with colors corresponding to the normalized RMSF values, indicated by the color bar on the right. Ligands (GTP) are shown as yellow sticks, residues within 5 Å of the ligands are shown as surfaces, and black boxes indicate their positions. The bottom panels display the RMSF of structures near the ligands separately, highlighting regions within the black boxes in the middle panels. b Results for 6P07. The top panel shows scatter plots of RMSF on residues, with colors corresponding to the three approaches as indicated in the legend. The middle panels present the visualizations of RMSF from the three approaches on the PDB structure, with colors corresponding to the normalized RMSF values, indicated by the color bar on the right. Ligands (ADP, ATP) are shown as yellow sticks, and residues within 5 Å of the ligands are shown as surfaces. The bottom panels display the RMSF of structures near the ligands separately.

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