BioExcel Building Blocks tutorials: Protein MD Setup (Gromacs Version)

BioExcel Building Blocks tutorials: Protein MD Setup (Gromacs Version) provide protocols to prepare protein systems (example Lysozyme, PDB 1AKI) for molecular dynamics simulations with GROMACS using the BioExcel Building Blocks (biobb) library.

Key Features:

• Step-by-Step Simulation Setup: A protocol for preparing a protein simulation system using Lysozyme (PDB 1AKI) as an illustrative example.
• BioExcel Building Blocks Library (biobb): A collection of Python wrappers that enable interoperable execution of biomolecular simulation tasks with GROMACS.
• Interoperability and Integration: Integration with software management tools to generate data ontologies, installation packages, and software containers and to enable use within workflow managers.
• Automation and Workflow Orchestration: Support for automated deployment systems and workflow orchestration to enable reproducible execution of simulation components.

Scientific Applications:

• Protein dynamics and interactions: Setup of MD simulations for studying conformational changes and intermolecular interactions at atomic resolution.
• Drug discovery and design: Preparation of protein targets for simulations used in ligand binding and stability assessments relevant to drug design.
• Protein function and stability studies: Generation of simulation-ready protein systems for investigations of folding, stability, and functional motions.
• Workflow integration for biomolecular simulation: Enabling incorporation of MD setup steps into automated, reproducible computational workflows.

Methodology:

Preparation of a protein simulation system (Lysozyme, PDB 1AKI) using BioExcel Building Blocks (biobb) Python wrappers, integration with software management tools to produce data ontologies, installation packages and containers, and support for automated deployment systems and workflow orchestration.