Human O-GlcNAc Transferase: Molecular Dynamics Trajectory of OGT-UDP-Peptide Complex

Piotr Sliz from Harvard University provides a molecular dynamics trajectory of the human O-GlcNAc transferase (OGT) complex. The simulation is based on the OGT?UDP?peptide complex (PDB 3PE4) and was performed using the Desmond software over a 1-microsecond timescale, taking 75 days to complete. The description details the preparation steps, forcefields used, and simulation conditions.

Use Cases

• Analyzing protein conformational changes based on the 1-microsecond molecular dynamics trajectory.
• Studying enzyme-substrate interactions based on the simulated OGT-UDP-peptide complex.
• Validating computational methods based on the detailed simulation protocol using CHARM27 and OPLS2001 forcefields.
• Visualizing molecular motion based on the processed trajectories intended for animation with VMD.

Strengths

• Simulation details are explicitly provided, including the 1-microsecond duration and 75-day runtime.
• The structural starting point is a known PDB entry (3PE4), providing a concrete origin.
• The description specifies the software (Desmond 2.2.9.1), forcefields (CHARM27, OPLS2001), and simulation conditions (300 K, 1 bar).

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

Piotr Sliz, Harvard University, via paperswithcode.

Collection Method

Molecular dynamics simulation performed using Desmond software on a 64-node Linux cluster.