alphafold

![header](imgs/header.jpg)

# AlphaFold

This package provides an implementation of the inference pipeline of AlphaFold
v2. For simplicity, we refer to this model as AlphaFold throughout the rest of
this document.

We also provide:

1.  An implementation of AlphaFold-Multimer. This represents a work in progress
    and AlphaFold-Multimer isn't expected to be as stable as our monomer
    AlphaFold system. [Read the guide](#updating-existing-installation) for how
    to upgrade and update code.
2.  The [technical note](docs/technical_note_v2.3.0.md) containing the models
    and inference procedure for an updated AlphaFold v2.3.0.
3.  A [CASP15 baseline](docs/casp15_predictions.zip) set of predictions along
    with documentation of any manual interventions performed.

Any publication that discloses findings arising from using this source code or
the model parameters should [cite](#citing-this-work) the
[AlphaFold paper](https://doi.org/10.1038/s41586-021-03819-2) and, if
applicable, the
[AlphaFold-Multimer paper](https://www.biorxiv.org/content/10.1101/2021.10.04.463034v1).

Please also refer to the
[Supplementary Information](https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-021-03819-2/MediaObjects/41586_2021_3819_MOESM1_ESM.pdf)
for a detailed description of the method.

**You can use a slightly simplified version of AlphaFold with
community-supported versions (see below).

If you have any questions, please contact the AlphaFold team at
[alphafold@deepmind.com](mailto:alphafold@deepmind.com).

![CASP14 predictions](imgs/casp14_predictions.gif)

## Installation and running your first prediction

You will need a machine running Linux, AlphaFold does not support other
operating systems. Full installation requires up to 3 TB of disk space to keep
genetic databases (SSD storage is recommended) and a modern NVIDIA GPU (GPUs
with more memory can predict larger protein structures).

Please follow these steps:

1.  Install [Docker](https://www.docker.com/).

    *   Install
        [NVIDIA Container Toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html)
        for GPU support.
    *   Setup running
        [Docker as a non-root user](https://docs.docker.com/engine/install/linux-postinstall/#manage-docker-as-a-non-root-user).

1.  Clone this repository and `cd` into it.

    ```bash
    git clone https://github.com/deepmind/alphafold.git
    cd ./alphafold
    ```

1.  Download genetic databases and model parameters:

    *   Install `aria2c`. On most Linux distributions it is available via the
        package manager as the `aria2` package (on Debian-based distributions
        this can be installed by running `sudo apt install aria2`).
        Same for `rsync`.

    *   Please use the script `scripts/download_all_data.sh` to download and set
        up full databases. This may take substantial time (download size is 556
        GB), so we recommend running this script in the background:

    ```bash