DeepAb is antibody structure prediction using interpretable deep learning.

References:

• JA Ruffolo, J Sulam, and JJ Gray Antibody structure prediction using interpretable deep learning Patterns (N Y). 2021 Dec 9;3(2):100406. doi: 10.1016/j.patter.2021.100406. eCollection 2022 Feb 11.

• DeepAb Main Site

• Module Name: deepab (see the modules page for more information)
• Multithreaded
• GPU-dependent (only the predict.py script)
• Environment variables set
  • DEEPAB_HOME
• Example files in $DEEPAB_HOME/data/sample_files

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

[user@biowulf]$ sinteractive --gres=gpu:p100:1 -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 deepab

[user@cn3144 ~]$ predict.py --decoys 4 --num_procs $SLURM_CPUS_ON_NODE --use_gpu --renumber \
--pred_dir $(pwd)/preds --model_dir $DEEPAB_HOME/trained_models/ensemble_abresnet \
$DEEPAB_HOME/data/sample_files/4h0h.fasta

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load deepab
predict.py --decoys 4 --num_procs $SLURM_CPUS_ON_NODE --use_gpu --renumber --pred_dir $(pwd)/preds --model_dir $DEEPAB_HOME/trained_models/ensemble_abresnet $DEEPAB_HOME/data/sample_files/4h0h.fasta

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=8 --mem=20g --gres=gpu:p100:1 deepab.sh

Create a swarmfile (e.g. deepab.swarm). For example:

annotate_attention.py --renumber --cdr_loop h3 --model_file $DEEPAB_HOME/trained_models/ensemble_abresnet/rs0.pt --out_file output_1.pdb sample_1.pdb
annotate_attention.py --renumber --cdr_loop h3 --model_file $DEEPAB_HOME/trained_models/ensemble_abresnet/rs0.pt --out_file output_2.pdb sample_2.pdb
annotate_attention.py --renumber --cdr_loop h3 --model_file $DEEPAB_HOME/trained_models/ensemble_abresnet/rs0.pt --out_file output_3.pdb sample_3.pdb
annotate_attention.py --renumber --cdr_loop h3 --model_file $DEEPAB_HOME/trained_models/ensemble_abresnet/rs0.pt --out_file output_4.pdb sample_4.pdb

Submit this job using the swarm command.

swarm -f deepab.swarm -g 10g -t 2 --module deepab