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Prodigy

Predicts the binding affinity of protein-protein complexes using structural and interface analysis.

Prodigy

Quick Start

  1. Prepare a PDB file of your protein complex.
  2. Specify the chains to analyze (e.g., A;B for two molecules).
  3. Set temperature and optional thresholds as needed.
  4. Run the node to obtain binding affinity metrics.

Setup Guide

1. Input Preparation

  1. Ensure your protein complex is in PDB format.
  2. Identify chain IDs for each molecule or group.

2. Node Configuration

  1. Enter the PDB structure and chain selection string.
  2. Adjust temperature, distance cutoff, and accessibility threshold as required.

Basic Usage

Binding Affinity Prediction

  • Predicts binding affinity (ΔG, Kd) for protein complexes.
  • Supports custom chain grouping for multi-chain complexes.
  • Outputs a CSV table with detailed interface metrics.

Configuration

Required Inputs

Field Description Type Example
pdb Target protein complex to predict binding affinity for. PDB complex.pdb
chains Chains to consider; semicolon separates molecules, comma groups chains. STRING A;B;C or A,B;C
temperature Temperature (°C) for Kd prediction. INT 25
distance_cutoff Distance cutoff (Å) to calculate interface contacts. FLOAT 5.5
acc_threshold Accessibility threshold for BSA analysis. FLOAT 0.05

Optional Inputs

None

Outputs

Field Description Example
score.csv Table with binding scores (binding_affinity, kd, contacts, contact_types, nis_a, nis_c, temperature) score.csv

Best Practices

Chain Selection

  • Use semicolons to separate different molecules (e.g., A;B).
  • Use commas to group chains as a single molecule (e.g., A,B;C).

Parameter Tuning

  • Adjust distance_cutoff and acc_threshold for specific interface definitions.
  • Set temperature to match experimental or physiological conditions.

Troubleshooting

Common Issues

  • Incorrect chain selection: Double-check chain IDs and grouping format.
  • Empty or invalid PDB input: Ensure the PDB file is valid and contains the specified chains.

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