ipSAE: for binders screening

Paper: What’s wrong with AlphaFold’s 𝑖𝑝𝑇𝑀 score and how to fix it https://doi.org/10.1101/2025.02.10.637595

Installation

pip install ipsae

Usage

Run ipSAE tool from the command line terminal in Linux. It takes the Alphafold2, Alphold3 and Boltz2 multimers PAE file in .json and .pdb or .cif file format as input, and distance cutoff values.

Command-line Help

$ ipsae --help

ipSAE
Scoring function for interprotein interactions
-------------------------------------------------
Version: 1.0
Author: Samee Ullah
Email: [email protected]
LinkedIn: https://www.linkedin.com/in/ullah-samee/
-------------------------------------------------
Based on the original work of Roland Dunbrack.

usage: ipsae [-h] pae_file structure_file [cutoffs ...]

Calculate ipSAE scores for protein-protein interactions

positional arguments:
  pae_file        PAE file (JSON or NPZ)
  structure_file  Structure file (PDB or CIF)
  cutoffs         Optional: PAE and distance cutoff values. Defaults are 15
                  for AF2 and 10 for AF3/Boltz1.

options:
  -h, --help      show this help message and exit

Examples:
For AlphaFold2:
  ipsae alphafold2_multimer.json alphafold2_model.pdb 15 15

For AlphaFold3:
  ipsae full_data_0.json model_0.cif 10 10

For Boltz:
  ipsae pae_model_0.npz Boltz_model.cif 10 10

Examples

AlphaFold2

ipsae scores.json model.pdb 15 15

default distance cutoffs of 15.

AlphaFold3

ipsae full_data_0.json model_0.cif 10 10

default distance cutoffs of 10.

Boltz1

ipsae pae_model_0.npz model_0.cif 10 10

default distance cutoffs of 10.

Output Files

The tool generates three output files:

1. <name>_<pae>_<dist>.txt: The main output file with chain-chain scores.
2. <name>_<pae>_<dist>_byres.txt: By-residue scores.
3. <name>_<pae>_<dist>.pml: A PyMOL script for visualizing the ipSAE scores.

Main Output File Format

The main output file contains a table with the following columns:

Chn1	Chn2	PAE	Dist	Type	ipSAE	ipSAE_d0chn	ipSAE_d0dom	ipTM_af	ipTM_d0chn	pDockQ	pDockQ2	LIS	n0res	n0chn	n0dom	d0res	d0chn	d0dom	nres1	nres2	dist1	dist2	Model

Credits

This tool is based on the original work of Roland Dunbrack.