FAIR Molecular Dynamics: Biomolecular Workflows with Metal Ion Precision

This use case aims to implement workflows designed to simulate the dynamics of biomolecular systems, with a particular emphasis on complex scenarios such as protein folding/unfolding, ligand binding, and small molecule diffusion into active sites. It should permit robustly handling multimolecular adducts, capturing transient and cooperative interactions between multiple biomolecules.
Special attention is given to metal ion coordination sites, incorporating accurate, possibly quantum-derived, parameters to reflect their unique electronic and bonding interactions. Non-standard residues, cofactors, and ligands are parameterized using advanced techniques that ensure compatibility with classical force fields.
The workflow integrates automated topology generation to allow users to address a wide range of molecular systems. Validation against experimental data ensures the reliability and transferability of the simulations across diverse biological contexts.

• Design an intuitive user interface (GUI/CLI) that simplifies system setup, parameter selection, and simulation launch, with guided workflows for common tasks.
• Automate complex parameterization steps, including detection and treatment of non-standard residues, metal-ion sites, and multimolecular assemblies.
• Implement standardized input/output formats and modular architecture to facilitate exchange with different simulation engines.
• Provide accessible documentation and training resources, including tutorials, example cases, and troubleshooting guides for users at all experience levels.
• Allow seamless deposition of parameters, data, results.

The workflow will enable accurate, reproducible simulations of complex biomolecular systems, including those with metal-ion centres and non-standard components. Users will be able to set up and launch simulations efficiently, with minimal manual intervention, across a wide range of biological scenarios.