PFDN4–Baicalein Complex: Molecular Dynamics Simulation Data from Two 100 ns Runs

Two independent 100 ns molecular dynamics simulations of the PFDN4 protein in complex with the ligand baicalein, performed by Weichao L and last updated on 2026-04-21. The 11.7 GB dataset includes trajectory files and analysis scripts tracking six specific pharmacophoric distances to assess binding stability. The data was generated in response to peer review to demonstrate ligand binding mode stability beyond global metrics.

Use Cases

• Validate protein-ligand binding stability based on specific pharmacophoric distance metrics described in the analysis.
• Compare the conformational dynamics of a ligand between two independent simulation runs with different initial velocities.
• Benchmark analysis methods for molecular dynamics trajectories that focus on local ligand interactions rather than global protein metrics.
• Study the interaction network of baicalein's functional groups (carbonyl, hydroxyls, aromatic rings) with specific PFDN4 active site residues.

Strengths

• Contains 200 ns of aggregate sampling from two independent 100 ns simulations.
• Analysis focuses on six specific pharmacophoric distances between ligand features and active site residues, as requested in peer review.
• Dataset is 11.7 GB, indicating a substantial volume of simulation data.

Limitations

• Row count and column-level documentation are unknown, which may limit suitability assessment.
• Description metadata is limited; actual data quality and structure require manual inspection after download.

Provenance

Source

figshare, author Weichao L

Collection Method

Molecular dynamics simulations performed with GROMACS, using AMBER14SB force field, TIP3P water, 300 K, NPT ensemble.

Freshness

Last updated 2026-04-21 04:18:23; freshness should be verified.