MDRepo-an open data warehouse for community-contributed molecular dynamics simulations of proteins

Area of Science:

• Biomolecular simulations
• Structural biology
• Computational chemistry

Background:

• Molecular Dynamics (MD) simulations offer critical insights into biomolecular behavior, including folding and interactions.
• Existing MD simulation data is scattered, lacking standardized metadata and access, hindering its use for machine learning.
• There is a need for a centralized, open-access repository for MD simulations.

Purpose of the Study:

• To introduce MDRepo, a novel infrastructure for storing and accessing MD simulations.
• To facilitate standardized community contribution and downstream analysis of simulation data.
• To enable efficient search, retrieval, and visualization of protein and protein-drug interaction simulations.

Main Methods:

• MDRepo is built on the open-source CyVerse cyber-infrastructure.
• It supports petabyte-scale storage with high-bandwidth upload/download.
• Provides a standardized process for data contribution and common analyses.

Main Results:

• MDRepo offers a robust solution for the scattered nature of MD simulation data.
• It enables standardized community contribution and access to simulations.
• The infrastructure supports large-scale data storage and retrieval.

Conclusions:

• MDRepo addresses the critical need for a centralized repository for molecular dynamics simulations.
• It provides a foundation for cloud-based access and advanced analyses, including machine learning.
• This repository will accelerate research in structural biology and drug discovery.