MDMoby

MDMoby provides programmatic access to molecular dynamics (MD) simulation workflows, enabling system preparation from PDB structures, execution with Amber, NAMD, and Gromacs, and trajectory analysis to support protein structure analysis, drug design, and biomolecular interaction studies.

Key Features:

• System Preparation: Prepares molecular systems starting from PDB structures using procedures that replicate expert manual preparation workflows.
• Integration with MD Packages: Supports execution of simulations with Amber, NAMD, and Gromacs.
• Trajectory Analysis Tools: Provides a suite of tools for analyzing MD trajectories using user-provided inputs and data from the MoDEL database.
• Programmatic Web-Services: Exposes BioMoby-based semantic web-services for programmatic interoperability and automated workflow integration.

Scientific Applications:

• Protein Structure Analysis: Enables preparation, simulation, and trajectory analysis to investigate protein conformational dynamics.
• Drug Design: Supports simulation and analysis workflows relevant to ligand binding, conformational sampling, and structure-based drug design studies.
• Biomolecular Interaction Studies: Facilitates investigation of protein–protein and protein–ligand interactions through MD simulation and trajectory analysis.

Methodology:

Uses semantic Web-Services implemented via BioMoby and incorporates a dedicated MD Ontology to represent semantic information and enable interoperability and data exchange between simulation and analysis tools.