MD simulations were limited to 100 ns duration, which may not be sufficient to capture long-timescale conformational changes or binding kinetics relevant to drug efficacy.

The gap

Consensus across the literature

Supporting evidence — 4 representative gaps

• A high-affinity split-HaloTag for live-cell protein labeling (2026) · doi

  MD simulations were limited to 200 ns at 300 K and 1.01325 bar; longer simulation times or varying conditions could provide additional insights into protein-ligand dynamics.

  Keywords: simulations limited longer simulation times varying conditions provide additional insights protein ligand dynamics
• Comprehensive pharmacokinetic profiling and binding stability assessment of phytochemicals from Aconitum heterophyllum against viral targets using in silico methods (2026) · doi

  While molecular docking was performed against 17 proteins from multiple viral diseases (HIV-AIDS, chikungunya, coronavirus, ebola, and herpes virus), the MD simulation was only conducted for the spike glycoprotein, leaving stability assessment incomplete for other target proteins.

  Keywords: proteins molecular docking performed against multiple viral diseases aids chikungunya coronavirus ebola herpes virus simulation
• Assessment of FDA-Approved Antiviral Drugs Indicated for Different Viral Infections Against Crimean-Congo Hemorrhagic Fever Virus: Molecular Docking and Molecular Dynamics Simulations (2026) · doi

  MD simulations were limited to 100 ns duration, which may not be sufficient to capture long-timescale conformational changes or binding kinetics relevant to drug efficacy.

  Keywords: simulations limited duration sufficient capture long timescale conformational changes binding kinetics relevant drug efficacy
• Computational molecular biology (2020) · doi

  The text emphasizes that molecular recognition and drug binding are dynamic processes involving conformational changes and 'jiggling' of both target and ligand, and that MD simulations reveal protein dynamics beyond X-ray crystallography. However, it does not specify quantitative thresholds for when protein flexibility significantly impacts docking predictions, benchmark datasets comparing static vs. dynamic docking performance, or guidelines for selecting force fields and simulation timescales for different protein classes in computational drug screening.

  Keywords: protein flexibility molecular dynamics simulations ligand binding docking force fields conformational changes