Molecular Dynamics Simulation Data for EFR3A and TCF12 Drug Complexes

Wei Lin's dataset contains raw data and scripts for 20-nanosecond molecular dynamics simulations of EFR3A‑cicloheximide and TCF12‑cicloheximide complexes. The 95.1 MB collection includes PDB structures, topology files, and analysis results for RMSD, RMSF, hydrogen bonds, and atomic distances. It was last updated on May 1, 2026, to support reproducibility for a study on allergic rhinitis and obstructive sleep apnea.

Use Cases

• Reproducing molecular dynamics simulation results based on provided GROMACS input and output files.
• Analyzing protein-ligand stability based on RMSD and RMSF data included in the dataset.
• Studying interaction dynamics based on hydrogen bond and key atomic distance analysis results.
• Developing or testing MD analysis scripts using the provided Python and R code.

Strengths

• Includes raw data for two independent 20 ns molecular dynamics replicates, supporting reproducibility.
• Provides multiple file formats (PDB, TOP, CSV, XVG) and analysis scripts for processing and plotting.
• Released under a permissive CC-BY-4.0 license, allowing for broad reuse and modification.

Limitations

• Row count and column-level documentation are absent; field semantics must be inferred after download.
• The 95.1 MB size indicates a relatively small dataset, which may limit the scope of analysis.
• Data may reflect the specific methodological bias inherent to the GROMACS software and force field parameters used.

Provenance

Source

figshare

Collection Method

Molecular dynamics simulations performed with GROMACS v2024.4, AMBER99SB-ILDN force field, and TIP3P water model.

Time Range

Simulation time of 20 nanoseconds per replicate.

Freshness

Last updated 2026-05-01 13:06:03; freshness should be verified.

Geography

null