AlphaFold 
Description
AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known
More information
- Homepage: https://deepmind.com/research/case-studies/alphafold
Available Versions of AlphaFold
Version | Module | Available on |
|---|---|---|
2.2.2-foss-2021a-CUDA-11.3.1 | bio/AlphaFold/2.2.2-foss-2021a-CUDA-11.3.1 | Noctua 2 |
This table is generated automatically. If you need other versions please click pc2-support@uni-paderborn.de.
Usage Hints for AlphaFold
If you need support in using this software or example job scripts please click pc2-support@uni-paderborn.de.
Example for Noctua 2
The following example shows the usage of Alphafold for t1050.fasta, which can be downloaded from https://predictioncenter.org/casp14/target.cgi?target=T1050&view=sequence.
It uses one Nvidia A100 GPU (40 GB) and runs for about 40 minutes.
#!/bin/bash
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --cpus-per-task=32
#SBATCH -p gpu
#SBATCH --gres=gpu:a100:1
module reset
module load bio/AlphaFold/2.2.2-foss-2021a-CUDA-11.3.1
rm -rf out
mkdir out
alphafold --data_dir=/scratch/data-repos/bio/AlphaFold/full_databases --fasta_paths=t1050.fasta --output_dir=out --max_template_date=2020-05-14 --model_preset=monomer --db_preset=reduced_dbs