diff --git a/apps/protein_folding/helixfold3/Dockerfile b/apps/protein_folding/helixfold3/Dockerfile
new file mode 100644
index 00000000..9b5cde31
--- /dev/null
+++ b/apps/protein_folding/helixfold3/Dockerfile
@@ -0,0 +1,40 @@
+ARG CUDA=12.8.1
+FROM nvidia/cuda:${CUDA}-cudnn-devel-ubuntu22.04
+# FROM directive resets ARGS, so we specify again (the value is retained if
+# previously set).
+ARG CUDA
+
+LABEL Author="j.caley@unsw.edu.au" \
+    title="helixfold3" \
+    description="Docker image containing all software requirements to run helixfold3"
+
+RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y wget git && \
+    wget -q -P /tmp "https://github.com/conda-forge/miniforge/releases/download/24.11.0-0/Miniforge3-$(uname)-$(uname -m).sh" && \
+    bash /tmp/Miniforge3-$(uname)-$(uname -m).sh -b -p /conda && \
+    git clone --filter=blob:none --no-checkout https://github.com/PaddlePaddle/PaddleHelix.git /app/helixfold3 && \
+    cd /app/helixfold3 && \
+    git sparse-checkout init --cone && \
+    git sparse-checkout set apps/protein_folding/helixfold3 && \
+    git checkout dev && \
+    mv apps/protein_folding/helixfold3/* . && \
+    rm -rf /tmp/Miniforge3-$(uname)-$(uname -m).sh /var/lib/apt/lists/* /root/.cache apps && \
+    apt-get remove --purge -y wget git && apt-get autoremove -y && apt-get clean -y
+
+COPY environment.yaml /app/helixfold3/environment.yaml
+
+ENV PATH="/conda/bin:$PATH"
+
+RUN mamba env create --file=/app/helixfold3/environment.yaml && \
+    mamba install -y -c bioconda aria2 hmmer==3.3.2 kalign2==2.04 hhsuite==3.3.0 -n helixfold && \
+    mamba install -y -c conda-forge openbabel -n helixfold && \
+    mamba clean --all --force-pkgs-dirs -y && \
+    rm -rf /root/.cache
+
+ENV PATH="/conda/bin:/app/helixfold3:./maxit_src/bin:/conda/envs/helixfold/bin:$PATH" \
+    RCSBROOT="./maxit_src" \
+    MAXIT_SRC="./maxit_src" \
+    PYTHON_BIN="/conda/envs/helixfold/bin/python3.9" \
+    ENV_BIN="/conda/envs/helixfold/bin" \
+    OBABEL_BIN="/conda/envs/helixfold/bin"
+
+ENTRYPOINT ["mamba", "run", "--name", "helixfold"]
diff --git a/apps/protein_folding/helixfold3/environment.yaml b/apps/protein_folding/helixfold3/environment.yaml
new file mode 100644
index 00000000..82833a68
--- /dev/null
+++ b/apps/protein_folding/helixfold3/environment.yaml
@@ -0,0 +1,35 @@
+name: helixfold
+channels:
+  - conda-forge
+  - bioconda
+  - nvidia
+  - biocore
+
+dependencies:
+  - python=3.9
+  - cuda-toolkit=12.0
+  - cudnn=8.4.0
+  - nccl=2.14
+  - libgcc=14.2.0
+  - libgomp=14.2.0
+  - pip=25.0.1
+  - aria2=1.37.0
+  - hmmer=3.4
+  - kalign2=2.04
+  - hhsuite=3.3.0
+  - openbabel=3.1.1
+  - pip:
+      - paddlepaddle-gpu==2.6.1 -f https://www.paddlepaddle.org.cn/whl/linux/mkl/avx/stable.html
+      - absl-py==0.13.0
+      - biopython==1.79
+      - chex==0.0.7
+      - dm-haiku==0.0.4
+      - dm-tree==0.1.6
+      - docker==5.0.0
+      - immutabledict==2.0.0
+      - jax==0.2.14
+      - ml-collections==0.1.0
+      - pandas==1.3.4
+      - scipy==1.9.0
+      - rdkit-pypi==2022.9.5
+      - posebusters==0.3.6
diff --git a/apps/protein_folding/helixfold3/helixfold3.def b/apps/protein_folding/helixfold3/helixfold3.def
new file mode 100644
index 00000000..957ec44e
--- /dev/null
+++ b/apps/protein_folding/helixfold3/helixfold3.def
@@ -0,0 +1,44 @@
+Bootstrap: docker
+From: nvidia/cuda:12.8.1-cudnn-devel-ubuntu22.04
+
+%labels
+    Author j.caley@unsw.edu.au
+    title="helixfold3"
+    description="Docker image containing all software requirements to run helixfold3"
+%files
+    environment.yaml /app/helixfold3/environment.yaml
+
+%post
+    apt update && DEBIAN_FRONTEND=noninteractive apt install --no-install-recommends -y wget git
+
+    wget -q -P /tmp "https://github.com/conda-forge/miniforge/releases/download/24.11.0-0/Miniforge3-$(uname)-$(uname -m).sh"
+    bash /tmp/Miniforge3-$(uname)-$(uname -m).sh -b -p /conda
+    rm /tmp/Miniforge3-$(uname)-$(uname -m).sh
+    export PATH="/conda/bin:$PATH"
+
+    git clone --filter=blob:none --no-checkout https://github.com/PaddlePaddle/PaddleHelix.git /app/helixfold3
+    cd /app/helixfold3
+    git sparse-checkout init --cone
+    git sparse-checkout set apps/protein_folding/helixfold3
+    git checkout dev
+    mv apps/protein_folding/helixfold3/* .
+    rm -rf apps
+
+    mamba env create --file=/app/helixfold3/environment.yaml
+    mamba install -y -c bioconda aria2 hmmer==3.3.2 kalign2==2.04 hhsuite==3.3.0 -n helixfold
+    mamba install -y -c conda-forge openbabel -n helixfold
+
+    apt autoremove -y && apt remove --purge -y wget git && apt clean -y
+    rm -rf /var/lib/apt/lists/* /root/.cache *.tar.gz
+    mamba clean --all --force-pkgs-dirs -y
+
+%environment
+    export PATH="/conda/bin:/app/helixfold3:./maxit_src/bin:/conda/envs/helixfold/bin:$PATH"
+    export RCSBROOT="./maxit_src"
+    export MAXIT_SRC="./maxit_src"
+    export PYTHON_BIN="/conda/envs/helixfold/bin/python3.9"
+    export ENV_BIN="/conda/envs/helixfold/bin"
+    export OBABEL_BIN="/conda/envs/helixfold/bin"
+
+%runscript
+    mamba run --name helixfold "$@"