Umol - Universal molecular framework

Structure prediction of protein-ligand complexes from sequence information

The protein is represented with a multiple sequence alignment and the ligand as a SMILES string, allowing for unconstrained flexibility in the protein-ligand interface. There are two versions of Umol: one that uses protein pocket information (recommended) and one that does not. Please see the runscript (predict.sh) for more information.

Read the paper here

Umol is available under the Apache License, Version 2.0. \ The Umol parameters are made available under the terms of the CC BY 4.0 license.

Colab (run Umol in the browser)

Colab Notebook

Local installation

(several minutes)

The entire installation takes <1 hour on a standard computer. \ We assume you have CUDA12. For CUDA11, you will have to change the installation of some packages. \ The runtime will depend on the GPU you have available and the size of the protein-ligand complex you are predicting. \ On an NVIDIA A100 GPU, the prediction time is a few minutes on average.

First install miniconda, see: https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html or https://docs.conda.io/projects/miniconda/en/latest/miniconda-other-installer-links.html

bash install_dependencies.sh

Run the test case

(a few minutes)

conda activate umol
bash predict.sh

Extract target positions from a pdb file of your choice

PDB_FILE=./data/test_case/7NB4/7NB4.pdb1
PROTEIN_CHAIN='A'
LIGAND_NAME='U6Q'
OUTDIR=./data/test_case/7NB4/
python3 ./src/parse_pocket.py --pdb_file $PDB_FILE \
--protein_chain $PROTEIN_CHAIN \
--ligand_name $LIGAND_NAME \
--outdir $OUTDIR

Citation

Bryant, P., Kelkar, A., Guljas, A. Clementi, C. and Noé F. Structure prediction of protein-ligand complexes from sequence information with Umol. Nat Commun 15, 4536 (2024). https://doi.org/10.1038/s41467-024-48837-6