Molecular Dynamics Side Chain Order Parameters and Trajectories for Ribonuclease H

Tab-delimited files report calculated S2 side chain order parameters for carboxyl- and carbonyl-containing residues (Asp, Glu, Asn, Gln) in RNase H homologs. The dataset also includes complete 100ns molecular dynamics trajectory data for E. coli RNase H under apo and magnesium-bound conditions, authored by Kate A. Stafford of Columbia University.

Use Cases

• Reproduce published figures (e.g., Figure 6 and Figure 8) based on the supplied order parameter data.
• Compare simulation and experimental results for protein side chain dynamics based on the provided S2 order parameters.
• Analyze molecular dynamics trajectories of E. coli RNase H based on the supplied 100ns DCD files.
• Investigate the structural effects of magnesium ion binding on RNase H based on the provided apo, site A, and site B simulation trajectories.

Strengths

• Includes complete 100ns molecular dynamics trajectories for three distinct E. coli RNase H simulation conditions.
• Provides calculated S2 order parameters for specific residue types across multiple RNase H homologs, sufficient to reproduce published figures.
• Contains equilibrated starting structures (PDB files) with all protein atoms and Mg ions explicitly included.

Limitations

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

Provenance

Source

Columbia University

Collection Method

Likely generated from molecular dynamics simulations and subsequent analysis.