bAIes-IDP - Ensembles of disordered proteins and multidomain proteins with Alphafold-2

Atomic resolution ensemble predictions of Intrinsically Disordered and Multi-domain Proteins with Alphafold-2

Here you can find scripts and tutorials to perform ensemble prediction of IDPs using Alphafold-2, as introduced in:

V. Schnapka, T. Morozova, S. Sen, M. Bonomi. Atomic resolution ensembles of intrinsically disordered with Alphafold. BioRxiv (2025). doi: https://doi.org/10.1101/2025.06.18.660298

This repository is organized in the following directories:

• scripts: python scripts used for preprocessing and preparations of the bAIes simulations.
• tutorials: complete tutorials for IDP ensemble preparation.
• benchmark: The input files to reproduce our simulations.
• installation: Some useful files to install the necessary software to run bAIes-IDP.

Software requirements

To run bAIes-IDP, you will need a linux workstation, a python environment and some softwares:

Alphafold-2

You can get Alphafold-2 here.

Alternatively, if you cannot run Alphafold-2 locally, you can use a version of Colabfold that outputs the distance distributions. An implementation can be found here.

A conda environment containing the intermol library

You can easily install this environment with conda by using the provided yml file (see installation) and running the following in a terminal:

conda env create -f baies.yml

Alternatively, the intermol library can be found here

GROMACS

GROMACS can be downloaded and installed from here

LAMMPS with PLUMED

LAMMPS version 2 Aug. 2023 source code can be downloaded here

For bAIes, LAMMPS must be patched with the file patch_cmap.txt provided in installation. After downloading the source code of LAMMPS, go in the source code main directory and run:

patch ./src/MOLECULE/fix_cmap.cpp < patch_cmap.txt

Then, LAMMPS can be compiled using CMake (described here) or using make (described here).

The implementation of PLUMED is described here.

We recommend the use of OpenMP for parallelization.