Molecular Dynamics Trajectories of Human β Defensin-3 in Model Lipid Membranes

Jackson Penfield's dataset contains molecular dynamics simulation trajectories for Human β defensin type 3 (hBD-3) monomers and dimers. The data comprises 57.0 microseconds of all-atom simulations across wild-type and analog protein forms embedded in four types of model lipid membranes. The dataset was last updated on April 30, 2026.

Use Cases

• Analyze protein conformational dynamics based on principal component analysis (PCA) and linear discriminant analysis (LDA) results.
• Investigate the effect of salt concentration on antimicrobial peptide structure based on contact matrices.
• Compare membrane interaction mechanisms between wild-type and analog protein forms.
• Study the ability of peptide dimers to distinguish between model Gram-positive and Gram-negative membranes.

Strengths

• Simulation data spans a total of 57.0 microseconds, which is a long timescale for all-atom molecular dynamics.
• Includes comparisons across four distinct types of model lipid membranes.
• Analyzes both monomer and dimer forms of the hBD-3 protein.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.

Provenance

Source

figshare

Collection Method

Data generated from long-time all-atom molecular dynamics simulations and subsequent trajectory analysis.

Time Range

The temporal coverage of the simulation data is not specified.

Freshness

Last updated 2026-04-30 15:36:23; freshness should be verified.

Geography

The spatial coverage is not applicable for this molecular simulation data.