AlphaFold

AlphaFold is a software package that provides an implementation of the inference pipeline of AlphaFold v2.0. This is a completely new model that was entered in CASP14 and pusblished in Nature.

Availability and Restrictions

Versions

Version Owens Pitzer
2.0.0   X
* Current default version

You can use module spider alphafold to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

AlphaFold is available for all OSC users

Publisher/Vendor/Repository and License Type

Copyright 2021 DeepMind Technologies Limited

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at https://www.apache.org/licenses/LICENSE-2.0. Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See hte License for the specific language governing permissions and limitations under the License. See the License for specific langauge governing permissions and limitations under the License.

The AlphaFold parameters are made available for non-commercial use only, under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) license. You can find details at: https://creativecommons.org/licenses/by-nc/4.0/legalcode.

 

Usage

Usage on Pitzer

Set-up on Pitzer

To load the default version of AlphaFold module, use module load alphafold.

Batch Usage on Pitzer

Below is the example batch script (job.txt) for an alphafold job:

#!/bin/bash
#SBATCH --ntasks=8
#SBATCH --gpus-per-node=2

module reset
module load alphafold/2.0.0

run_alphafold.sh --preset=reduced_dbs --fasta_paths=rcs_pdb_6VR4.fasta --max_template_date=2020-05-14 --output_dir=$(pwd -P)/output

Other available job options are:

--preset=recued_dbs, --preset=full_dbs, or --preset=casp14

 

Further Reading

Online documentation is available on the AlphaFold homepage.

Notes on AlphaFold output.

Notes on citing AlphaFold.

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