AlphaFold3正式开源：本地部署指南

1. 首先，确认硬件要求：

• 需要 Linux 操作系统

• 需要 NVIDIA GPU (计算能力 8.0 或更高)

• 至少 64GB RAM

• 推荐 1TB SSD 存储空间

• 推荐使用 NVIDIA A100 或 H100 GPU (80GB 显存)

安装基础软件：

# 安装必要的包sudo apt-get updatesudo apt-get install -y ca-certificates curl git
# 安装 Dockersudo apt-get install ca-certificates curlsudo install -m 0755 -d /etc/apt/keyringssudo curl -fsSL https://download./linux/ubuntu/gpg -o /etc/apt/keyrings/docker.ascsudo chmod a r /etc/apt/keyrings/docker.asc
# 添加 Docker 仓库echo \ 'deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] https://download./linux/ubuntu \ $(. /etc/os-release && echo '$VERSION_CODENAME') stable' | \ sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
# 安装 Dockersudo apt-get updatesudo apt-get install -y docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin

安装 NVIDIA 驱动和 Docker GPU 支持：

# 安装 NVIDIA 驱动sudo apt-get -y install alsa-utils ubuntu-drivers-commonsudo ubuntu-drivers installsudo nvidia-smi --gpu-reset
# 安装 NVIDIA Docker 支持curl -fsSL https://nvidia./libnvidia-container/gpgkey | sudo gpg --dearmor -o /usr/share/keyrings/nvidia-container-toolkit-keyring.gpgcurl -s -L https://nvidia./libnvidia-container/stable/deb/nvidia-container-toolkit.list | \  sed 's#deb https://#deb [signed-by=/usr/share/keyrings/nvidia-container-toolkit-keyring.gpg] https://#g' | \  sudo tee /etc/apt/sources.list.d/nvidia-container-toolkit.listsudo apt-get updatesudo apt-get install -y nvidia-container-toolkit

获取 AlphaFold 3 源代码：

git clone https://github.com/google-deepmind/alphafold3.gitcd alphafold3

下载数据库：

# 创建数据库目录mkdir -p $HOME/alphafold_db# 下载数据库python3 fetch_databases.py --download_destination=$HOME/alphafold_db

获取模型参数：

• 通过 Google 提供的表单申请访问权限

• 等待审核通过(2-3个工作日)

• 下载模型参数到指定目录(比如 $HOME/alphafold_params)

建立 Docker 容器：

docker build -t alphafold3 -f docker/Dockerfile .

准备运行环境：

# 创建输入输出目录mkdir -p $HOME/af_inputmkdir -p $HOME/af_output
# 创建输入文件cat > $HOME/af_input/fold_input.json << EOF{  'name': '2PV7',  'sequences': [    {      'protein': {        'id': ['A', 'B'],        'sequence': 'GMRESYANENQFGFKTINSDIHKIVIVGGYGKLGGLFARYLRASGYPISILDREDWAVAESILANADVVIVSVPINLTLETIERLKPYLTENMLLADLTSVKREPLAKMLEVHTGAVLGLHPMFGADIASMAKQVVVRCDGRFPERYEWLLEQIQIWGAKIYQTNATEHDHNMTYIQALRHFSTFANGLHLSKQPINLANLLALSSPIYRLELAMIGRLFAQDAELYADIIMDKSENLAVIETLKQTYDEALTFFENNDRQGFIDAFHKVRDWFGDYSEQFLKESRQLLQQANDLKQG'      }    }  ],  'modelSeeds': [1],  'dialect': 'alphafold3',  'version': 1}EOF

运行 AlphaFold 3：

docker run -it \ --volume $HOME/af_input:/root/af_input \ --volume $HOME/af_output:/root/af_output \ --volume $HOME/alphafold_params:/root/models \ --volume $HOME/alphafold_db:/root/public_databases \ --gpus all \ alphafold3 \python run_alphafold.py \ --json_path=/root/af_input/fold_input.json \ --model_dir=/root/models \ --output_dir=/root/af_output

表单申请访问地址：https://docs.google.com/forms/d/e/1FAIpQLSfWZAgo1aYk0O4MuAXZj8xRQ8DafeFJnldNOnh_13qAx2ceZw/viewform

GitHub仓库地址：https://github.com/google-deepmind/alphafold3/tree/main