MolDy

MolDy performs end-to-end molecular dynamics simulations using GROMACS to study the structure, folding, and inter-molecular interactions of biological macro and micro molecules.

Key Features:

• Trajectory Analysis: The tool analyzes simulation trajectories and generates graphical representations of relevant biophysical parameters.
• Customizable Parameters: MolDy provides valid default prefilled parameters for beginners while allowing modifications for expert users.
• Python and Perl Backend: The application integrates a Python and Perl-based logical backend that connects the Linux shell and Gromacs software.

Scientific Applications:

• Structural Biology: MolDy enables computational experiments to understand the structure of biological macro and micro molecules.
• Protein Folding Studies: The tool investigates the folding mechanisms of biological molecules.
• Inter-molecular Interaction Analysis: MolDy elucidates inter-molecular interactions relevant to macromolecular function.
• Drug Development: Accurate structural knowledge from simulations supports drug development pipelines.

Methodology:

MolDy connects to GROMACS through a Python and Perl-based backend interfacing with the Linux shell.