compbio-diffdock-docking

What problem does it solve?

This Skill provides a turnkey toxin-receptor docking benchmark using DiffDock and RDKit. It automates the generation of toxin–receptor pairs, fills SMILES strings, assigns PDB IDs and experimental Kd values, and compiles detailed binding-mode descriptions to support reproducible structural biology evaluations.

Core Features & Use Cases

• Automated benchmarking workflow that ingests toxin-receptor pairs and outputs standardized docking data (SMILES, PDB IDs, Kd, and binding-mode narratives).
• Deterministic, repeatable results suitable for validation, comparison across models, and educational demonstrations in pharmacology and structural biology.
• Validation constraints integrated into the workflow, including pharmacological relevance of Kd and informative binding-mode descriptions.

Quick Start

Run the DiffDock docking benchmark using the included toxin_benchmarks.json to generate and review SMILES, PDB IDs, Kd values, and binding-mode descriptions.