HpTonB(30-285) Protein Molecular Dynamics Simulation Trajectories

Molecular dynamics simulation trajectories of the periplasmic part of the TonB protein from Helicobacter pylori. The data includes the last 1000 nanoseconds of simulation performed with the Amber ff03ws force field in a 150 mM NaCl solution. I. Salla Virtanen from the University of Helsinki generated this dataset, which is available via paperswithcode.

Use Cases

• Analyzing protein conformational dynamics based on the 1000-nanosecond trajectory.
• Validating or benchmarking the Amber ff03ws force field based on the described simulation parameters.
• Studying protein-solvent interactions based on the availability of trajectories containing solvent.
• Investigating ion-protein interactions based on the inclusion of 150 mM NaCl in the simulation.

Strengths

• Trajectory data covers a substantial 1000-nanosecond simulation segment.
• Simulation uses a specific, documented force field (Amber ff03ws) and salt concentration (150 mM NaCl).
• Provides multiple file versions, including protein-only and solvent-containing trajectories.

Limitations

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

Provenance

Source

University of Helsinki

Collection Method

Molecular dynamics simulation using the Amber ff03ws force field.