# Binding Affinity Prediction Prodigy

> Protein complex binding affinity prediction. Use this skill when: (1) Predict the binding affinity score, (2) Using protein complex structure.

- Skill: `pharmolix/binding-affinity-prediction-prodigy` (Agent Skill)
- Install (CLI): `npx skillmds@latest add pharmolix/binding-affinity-prediction-prodigy`
- Raw SKILL.md: https://api.skillmd.com/api/skills/pharmolix/binding-affinity-prediction-prodigy/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- License: MIT
- Author: pharmolix (https://skillmd.com/u/pharmolix)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/pharmolix/binding-affinity-prediction-prodigy

---


# Prodigy Binding Affinity Prediction for Protein Complex

## Prerequisites

| Requirement | Minimum | Recommended |
|-------------|---------|-------------|
| Python | 3.10+ | 3.10 |
| RAM | 32GB | 64GB |

## How to run

### Local installation
```bash
pip install prodigy-prot
```

### Predict binding affinity of a protein complex structure
```python
import os 

def pred_binding_affinity(complex_pdb_file, distance_cutoff=5.5):
    """
    :param complex_pdb_file: path to the protein complex structure file
    :param distance_cutoff: distance cutoff to calculate ICs
    :return binding affinity score for protein complex
    """

    command = [
        'prodigy', pdb_file,
        '--distance-cutoff', distance_cutoff
    ]

    try:
        output = subprocess.run(command, capture_output=True, text=True).stdout.split("##########################################")[1]
        score = output.split("[++] Predicted binding affinity (kcal.mol-1):")[1].split("\n")[0] 
    except:
        output = "No contacts found for selection"
        score = "0.0"

    return float(score.strip())

# Predict binding affinity score for protein complex (PDB file)
binding_affinity_score = pred_binding_affinity(complex_pdb_file)
```

## Decision tree

```
Should I use Prodigy?
│
└─ What type of complex are evaluated?
   ├─ Protein complex → binding-affinity-prediction-prodigy ✓
   └─ Protein-ligand complex → structure-prediction-boltz-2
```