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Updated: Jun 6, 2026
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Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies
Published on: September 1, 2023
MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories
Tim Meyer1, Marco D'Abramo, Adam Hospital
1Joint IRB-BSC Computational Biology Programme, Institute of Research in Biomedicine, Parc Científic de Barcelona, Baldiri Reixac 10, Barcelona 08028, Spain.
Structure (London, England : 1993)
|November 13, 2010
Summary
State-of-the-art simulations provide over 1700 protein trajectories, stored in a data warehouse for querying dynamic protein information and interactions. This resource aids in understanding protein flexibility properties.
Area of Science:
- Biophysics
- Computational Biology
- Structural Biology
Background:
- Understanding protein dynamics is crucial for deciphering biological function.
- The Protein Data Bank (PDB) archives static protein structures, but dynamic information is less accessible.
- Molecular dynamics simulations offer insights into protein flexibility and interactions.
Purpose of the Study:
- To present a comprehensive database of protein dynamics derived from extensive molecular dynamics simulations.
- To provide a queryable resource for accessing dynamic information on monomeric soluble proteins.
- To demonstrate the utility of the database for characterizing global protein flexibility.
Main Methods:
- Atomistic molecular dynamics (MD) simulations were performed under near-physiological conditions.
- Over 1700 trajectories of proteins representative of monomeric soluble structures were generated.
- A large data warehouse was established to store and manage simulation data and analyses.
- Web server access is provided for basic analyses and reduced-resolution trajectories.
Main Results:
- A substantial dataset of protein trajectories and associated analyses is now available.
- The database enables querying for dynamic protein information, including interaction data.
- Examples illustrate the application of the database in assessing protein global flexibility properties.
- Accessible data includes solvent-stripped trajectories at a reduced resolution.
Conclusions:
- The developed database represents a significant resource for studying protein dynamics.
- It facilitates the investigation of protein flexibility and interactions through queryable simulation data.
- The web server provides convenient access to essential dynamic information for researchers.
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