BioBB-Wfs

BioBB-Wfs executes and manages biomolecular simulation workflows including molecular dynamics setup, protein–ligand docking, trajectory analysis, and small molecule parameterization using BioExcel Building Blocks components.

Key Features:

• Preconfigured Biomolecular Simulation Workflows: Provides workflows for molecular dynamics setup, protein–ligand docking, trajectory analysis, and small molecule parameterization.
• Integration with BioExcel Building Blocks: Implements workflows using the modular BioExcel Building Blocks (BioBB) library.
• Interactive Structural Visualization: Integrates the NGL viewer for three-dimensional biomolecular structure visualization.
• Molecular Dynamics Trajectory Analysis: Uses MDsrv for interactive analysis and exploration of molecular dynamics trajectories.
• Interactive Data Visualization: Generates two-dimensional analytical plots using Plotly.
• Remote Workflow Execution: Supports execution of biomolecular simulations on remote high-performance computing resources using user-provided credentials.

Scientific Applications:

• Molecular Dynamics Simulation Preparation: Prepares and executes molecular dynamics simulations of biomolecular systems.
• Protein–Ligand Docking Studies: Performs docking analyses to investigate protein–ligand interactions.
• Trajectory and Structural Analysis: Analyzes molecular dynamics trajectories and structural changes in biomolecules.
• Small Molecule Parameterization: Generates molecular parameters required for simulation of small molecules.

Methodology:

BioBB-Wfs executes preconfigured biomolecular simulation workflows implemented with BioExcel Building Blocks, performs molecular dynamics setup, docking, and trajectory analyses, and integrates visualization through NGL viewer, MDsrv, and Plotly.