PTX3 Molecular Dynamics Simulation Outputs for Apo and Ligand-Bound States

38.9 MB of molecular dynamics simulation files for the protein PTX3, including triplicate runs for its apo state and two ligand-bound complexes. The dataset contains analyses for backbone RMSD, ligand RMSD, RMSF, radius of gyration, SASA, hydrogen bonds, PCA, and MMPBSA free energy calculations. Author MAYANK DEEP SINGH uploaded these GROMACS outputs under a CC-BY-4.0 license to support reproducibility in studying PTX3-ligand binding for cardiovascular disease.

Use Cases

• Assess structural stability and conformational dynamics based on backbone RMSD and RMSF analyses mentioned in the description
• Calculate binding energetics and compare ligand affinities based on MMPBSA free energy calculations mentioned in the description
• Analyze protein compactness and solvent exposure based on radius of gyration and SASA data mentioned in the description
• Investigate ligand binding pose stability based on ligand RMSD trajectories mentioned in the description
• Perform dimensionality reduction and identify major conformational modes based on principal component analysis mentioned in the description

Strengths

• Triplicate simulations for each state (apo, complex A, complex B) enhance statistical reliability.
• Includes multiple standard MD analyses (RMSD, RMSF, Rg, SASA, H-bonds, PCA, FEL, MMPBSA) for a comprehensive view.
• Simulations performed with explicit solvent conditions and standard GROMACS workflows, as described.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment for large-scale ML tasks.
• The 38.9 MB size suggests a small dataset, potentially limiting the scope of downstream analysis.

Provenance

Source

figshare

Collection Method

Generated via GROMACS molecular dynamics simulations, including energy minimization, equilibration, and production runs.

Freshness

Last updated 2026-05-11 07:56:55; freshness should be verified.