CXCR2-Navarixin Complex: Three Independent 100 ns Molecular Dynamics Replicates

Three independent 100 ns molecular dynamics simulations of the CXCR2-Navarixin complex provide raw trajectories for analysis. The dataset includes initial and final PDB structures, full trajectories, and force field topology files for both protein and ligand. Neng Zhang published this data on figshare in May 2026 to support findings in a manuscript on shared molecular signatures in pulmonary and pleural diseases.

Use Cases

• Validate protein-ligand binding stability based on the 100 ns trajectory data mentioned in the description
• Analyze conformational changes in the CXCR2 receptor based on the provided PDB structures
• Benchmark force field parameters (Amber99SB-ILDN, GAFF2) based on the included topology files
• Train machine learning models for binding affinity prediction based on the raw simulation trajectories

Strengths

• Contains three independent 100 ns simulation replicates, allowing for robustness checks
• Includes both structural data (PDB files) and full trajectory data (XTC files)
• Provides explicit force field topology files for the protein (Amber99SB-ILDN) and ligand (GAFF2)

Limitations

• Column-level documentation is absent; field semantics must be inferred after download
• Row count is unknown, which may limit suitability assessment
• Data may reflect methodological bias inherent to the specific simulation setup

Provenance

Source

Neng Zhang

Collection Method

Molecular dynamics simulation

Freshness

Last updated 2026-05-28 18:40:16; freshness should be verified