Molecular Dynamics Parameters and MM-GBSA Binding Free Energy Calculations

Hriddhi Sarker's dataset provides molecular dynamics simulation parameters and MM-GBSA binding free energy calculations for protein–ligand complexes. The data includes standard error of the mean (SEM) values for the calculated energies. It was last updated on June 1, 2026, and is shared under a CC-BY-4.0 license.

Use Cases

• Benchmarking molecular docking software based on calculated MM-GBSA binding free energies.
• Analyzing the relationship between simulation parameters and binding affinity predictions based on the described data.
• Training or validating machine learning models for binding energy estimation based on molecular dynamics-derived features.

Strengths

• Includes standard error of the mean (SEM) for calculated binding energies, providing uncertainty estimates.
• Shared under a permissive CC-BY-4.0 license for open reuse.

Limitations

• Dataset is very small at 5.5 KB, indicating limited scope.
• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.

Provenance

Source

Hriddhi Sarker via figshare

Collection Method

Likely generated from computational molecular dynamics simulations and MM-GBSA calculations.

Freshness

Last updated 2026-06-01 17:47:04; freshness should be verified.