binding-affinity-prediction-prodigy

name	binding-affinity-prediction-prodigy
description	Protein complex binding affinity prediction. Use this skill when: (1) Predict the binding affinity score, (2) Using protein complex structure.
license	MIT
category	design-tools
tags	["binding affinity","protein complex"]

Prodigy Binding Affinity Prediction for Protein Complex

Prerequisites

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

How to run

Local installation

pip install prodigy-prot

Predict binding affinity of a protein complex structure

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