alphafold2: A Python repository from sailfish009

Alphafold2 - Pytorch (wip)

To eventually become an unofficial working Pytorch implementation of Alphafold2. Will be gradually implemented as more details of the architecture is released.

If you are interested in replication efforts, please drop by #alphafold at this Discord channel

Install

$ pip install alphafold2-pytorch

Usage

import torch
from alphafold2_pytorch import Alphafold2

model = Alphafold2(
    dim = 256,
    depth = 2,
    heads = 8,
    dim_head = 64
).cuda()

seq = torch.randint(0, 21, (1, 128)).cuda()
msa = torch.randint(0, 21, (1, 5, 64)).cuda()
mask = torch.ones_like(seq).bool().cuda()
msa_mask = torch.ones_like(msa).bool().cuda()

distogram = model(
    seq,
    msa,
    mask = mask,
    msa_mask = msa_mask
) # (1, 128, 128, 37)

Data

This library will use the awesome work by Jonathan King at this repository.

To install

$ git clone https://github.com/jonathanking/sidechainnet.git
$ cd sidechainnet && pip install -e .

Speculation

https://fabianfuchsml.github.io/alphafold2/

https://moalquraishi.wordpress.com/2020/12/08/alphafold2-casp14-it-feels-like-ones-child-has-left-home/

Developments from competing labs

https://www.biorxiv.org/content/10.1101/2020.12.10.419994v1.full.pdf

Final step - Fast Relax

Citations

@misc{unpublished2021alphafold2,
    title={Alphafold2},
    author={John Jumper},
    year={2020},
    archivePrefix={arXiv},
    primaryClass={q-bio.BM}
}

@misc{king2020sidechainnet,
    title={SidechainNet: An All-Atom Protein Structure Dataset for Machine Learning}, 
    author={Jonathan E. King and David Ryan Koes},
    year={2020},
    eprint={2010.08162},
    archivePrefix={arXiv},
    primaryClass={q-bio.BM}
}

@misc{alquraishi2019proteinnet,
    title={ProteinNet: a standardized data set for machine learning of protein structure}, 
    author={Mohammed AlQuraishi},
    year={2019},
    eprint={1902.00249},
    archivePrefix={arXiv},
    primaryClass={q-bio.BM}
}