Boltz-1 is the state-of-the-art open-source model to predict biomolecular structures containing combinations of proteins, RNA, DNA, and other molecules. It also supports modified residues, covalent ligands and glycans, as well as conditioning the prediction on specified interaction pockets or contacts.

References:

• Wohlwend J, Corso G, Passaro S, Reveiz M, Leidal K, Swiderski W, Portnoi T, Chinn I, Silterra J, Jaakkola T, Barzilay R. Boltz-1 Democratizing Biomolecular Interaction Modeling. bioRxiv [Preprint]. 2024 Dec 27:2024.11.19.624167. doi: 10.1101/2024.11.19.624167. PMID: 39605745; PMCID: PMC11601547. PubMed |  Journal

• boltz Main Site

• Please change the cache directory (the default setting will fill up $HOME directory quickly) with:

  --cache /data/$USER/boltz

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --gres=lscratch:30,gpu:a100:1 -c 8 --mem=20g  
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load boltz

[user@cn3144 ~]$ cd /data/$USER/
[user@cn3144 ~]$ cp -r {$BOLTZ_EXAMPLES:-none} .

[user@cn3144 ~]$ boltz predict ./examples/ligand.yaml --cache /data/$USER/boltz

Create a batch input file (e.g. boltz.sh). For example:

#!/bin/bash
set -e
module load boltz
boltz predict ./examples/ligand.yaml --cache /data/$USER/boltz

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=6 --mem=20g --gres=lscratch:30,gpu:a100:1 --partition=gpu boltz.sh