In-Depth Protein–Ligand Dynamics Review
Graphical abstract
Summary
Trajectory stability, contact persistence and conformational overlays jointly describe the main dynamic features of the protein–ligand complex in explicit solvent. The graphical abstract aligns representative poses, key contacts and cross-condition comparisons so interaction patterns can be reviewed quickly. The combined results establish pose priorities and actionable interaction leads. The result-focused presentation supports efficient review of the main evidence and research priorities.
Computational results
Computational Results
Figure 1. Molecular docking and molecular dynamics (MD) simulation analysis of protein-rich complexes. (A) The total binding conformation of the small molecule in the protein binding pocket, with a local enlargement diagram on the right of the binding point, showing the patterns of interactions between the critical residue and ligand, the green void representing the action of hydrogen bonds, the gray void represents the action to drain the hydrogen bond, and the orange void the pi-pi action; (B) the two-dimensional interaction between the ligand and the critical amino acid residue; (C) the protein、ligand and complex simulation in 100 ns molecular dynamics (MD) Changes in RMSD during tion; (D) RMSF distribution of protein main chain residues; (E) complex changes in radius of gyration during simulation; (Rg) changes in the surface area of solvent F) complex change over time; (G) changes of the distance between ligand mass and protein mass; (H) changes to the purpose of hydrogen bonds between protein ligand during simulated process; (I) analysis of the energy contribution of the critical amino acid residues to approximate binding free energy; (J) a two-dimensional projection map of the free-energy landscape (FEL) built on the basis of RMSD and Rg; (K) a static electricity distribution map of protein surfaces; (M) a complexconformation superimposition map of molecular dynamics (MD) simulation at 0 ns、50 ns and 100 ns.
This figure presents the principal structures and trends in “Computational Results” and connects them to the case-level ranking and result interpretation.
Full case PDF
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