MDWeb

MDWeb provides a web-based platform for preparing, executing, and analyzing molecular dynamics (MD) simulations and exposes programmatic services via MDMoby using the BioMoby framework.

Key Features:

• System Preparation: Prepares molecular systems from Protein Data Bank (PDB) structures by emulating expert-level protocols.
• Simulation Execution: Generates inputs for and interfaces with Amber, NAMD, and Gromacs to run MD simulations.
• Trajectory Analysis: Provides trajectory analysis using built-in tools, user-supplied tools, or methods available in the MoDEL database.
• High-throughput Support: Supports both standard and high-throughput simulation settings for large-scale studies.
• Programmatic Access (MDMoby): Exposes platform functionality as web services via MDMoby based on the BioMoby framework for integration into workflows.

Scientific Applications:

• Drug discovery: Enables MD simulations applicable to drug discovery workflows.
• Protein–ligand interaction studies: Supports simulation and analysis of protein–ligand binding and dynamics.
• Molecular mechanism investigation: Facilitates studies of fundamental biological processes at the molecular level.
• High-throughput MD studies: Enables large-scale or ensemble simulation studies for comparative and statistical analyses.

Methodology:

System preparation from PDB structures by emulating expert procedures; generation of simulation inputs and execution with Amber, NAMD, and Gromacs; trajectory analysis via built-in or user tools and methods from the MoDEL database; programmatic access provided through MDMoby using the BioMoby framework.