MoDEL

MoDEL stores molecular dynamics (MD) simulations of monomeric soluble protein structures from the Protein Data Bank (PDB), comprising over 1700 atomistic trajectories generated under near-physiological conditions to support analysis of protein dynamics, flexibility, and interactions (Publication 1, PMID: 21070939).

Key Features:

• Extensive trajectory collection: Contains more than 1700 molecular dynamics trajectories representing structural clusters of monomeric soluble proteins derived from the PDB.
• Atomistic simulations: Trajectories were produced by atomistic molecular dynamics simulations performed under near-physiological conditions.
• Dynamic information warehouse: Stores dynamic properties including interaction patterns and protein flexibility metrics for each trajectory.
• Processed trajectory variants: Includes trajectory versions with solvent molecules removed and trajectories at reduced resolution for simplified analyses.
• Basic analyses: Provides basic derived analyses computed from the stored trajectories.

Scientific Applications:

• Protein flexibility analysis: Enables study of global and local flexibility properties derived from atomistic MD trajectories.
• Interaction studies: Supports analysis of protein interaction patterns and dynamic behavior under near-physiological conditions.

Methodology:

Trajectories were generated by atomistic molecular dynamics simulations under near-physiological conditions, organized into structural clusters, and stored along with processed variants (solvent-removed and reduced-resolution) and basic derived analyses.