compbio-openmm-simulation

What problem does it solve?

Automates end-to-end toxin–receptor molecular dynamics simulations using OpenMM + RDKit, filling SMILES structures, UniProt targets, binding site residues, and detailed toxicity mechanisms for use in computational toxicology and structural biology.

Core Features & Use Cases

• Auto-fills toxin data (SMILES, target, UniProt, binding site residues, mechanism, LD50) for ready MD workflows.
• Validate toxin data with strict frontmatter and validation rules to ensure realistic, toxically focused parameters.
• Use cases include screening lethal toxins and studying mechanism-of-action via OpenMM simulations with RDKit support.

Quick Start

Provide toxin data (name, SMILES, target protein, UniProt accession, binding site residues, mechanism of action, and LD50) to generate a complete OpenMM-based MD workflow.