Journal: Bioresources and Bioprocessing

Article Title: Traditional processing unlocks anti-atherogenic potential of perilla fruit via PPAR-γ activation by luteolin

doi: 10.1186/s40643-025-00957-7

Figure Lengend Snippet: A : Molecular dynamics RMSD changes of the complex of luteolin and PPAR-γ within 100 ns; B : The RMSF position of the complex of luteolin and PPAR-γ; C : Protein Ligand contacts of the complex of luteolin and PPAR-γ, where green represents hydrogen bonds, purple represents hydrophobic bonds, and blue represents water bridges; D : Timeline representation of the interactions and contacts

Article Snippet: Fig. 4 A : Molecular dynamics RMSD changes of the complex of luteolin and PPAR-γ within 100 ns; B : The RMSF position of the complex of luteolin and PPAR-γ; C : Protein Ligand contacts of the complex of luteolin and PPAR-γ, where green represents hydrogen bonds, purple represents hydrophobic bonds, and blue represents water bridges; D : Timeline representation of the interactions and contacts

Techniques:

Journal: Drug Design, Development and Therapy

Article Title: Detailed in silico Evaluation of WNV Proteins: Dynamic and Thermodynamic Insights into Doravirine as a Potential Multitarget Agent

doi: 10.2147/DDDT.S551496

Figure Lengend Snippet: Molecular Dynamics analysis assessing protein backbone stability over the course of the simulation, based on Root Mean Square Deviation (RMSD) calculations for the core protein. Stability was evaluated by comparing RMSD profiles of the apo form with those of the protein bound to the analyzed compounds within the C-terminal tunnel ( A ) and the N-terminal hydrophobic pocket ( B ). At the bottom of the panel, the structural superimposition of the final simulation frames shows the apo core protein (gray) overlaid with the structures bound to remdesivir (red), rilpivirine (green), and doravirine (purple) in its N-terminal hydrophobic pocket (outlined in dashed circle).

Article Snippet: Figure 5 Molecular Dynamics analysis assessing protein backbone stability over the course of the simulation, based on Root Mean Square Deviation (RMSD) calculations for the core protein.

Techniques:

Journal: Drug Design, Development and Therapy

Article Title: Detailed in silico Evaluation of WNV Proteins: Dynamic and Thermodynamic Insights into Doravirine as a Potential Multitarget Agent

doi: 10.2147/DDDT.S551496

Figure Lengend Snippet: Molecular Dynamics analysis assessing protein backbone stability over the course of the simulation, based on Root Mean Square Deviation (RMSD) calculations for the RdRp NS5 protein. Stability was evaluated by comparing RMSD profiles of the apo form with those of the protein bound to the analyzed compound within the RdRp domain of NS5.

Article Snippet: Figure 5 Molecular Dynamics analysis assessing protein backbone stability over the course of the simulation, based on Root Mean Square Deviation (RMSD) calculations for the core protein.

Techniques:

Journal: Drug Design, Development and Therapy

Article Title: Detailed in silico Evaluation of WNV Proteins: Dynamic and Thermodynamic Insights into Doravirine as a Potential Multitarget Agent

doi: 10.2147/DDDT.S551496

Figure Lengend Snippet: Molecular Dynamics analysis assessing protein backbone stability over the course of the simulation, based on Root Mean Square Deviation (RMSD) calculations for the MTase NS5 protein. Stability was evaluated by comparing RMSD profiles of the apo form with those of the protein bound to the analyzed compounds within the SAH site ( A ) and KDKE motif ( B ). In panel A (bottom), structural superimposition of the final MD frames shows the apo NS5 MTase (yellow) overlaid with the rilpivirine-bound structure (green), with the cofactor depicted as a purple ball-and-stick. The Asp36–Val49 loop region, exhibiting a conformational shift, is highlighted by a dashed circle.

Article Snippet: Figure 5 Molecular Dynamics analysis assessing protein backbone stability over the course of the simulation, based on Root Mean Square Deviation (RMSD) calculations for the core protein.

Techniques: