From c490e54afe67adffecf6be244cc4cd7d6e5a7523 Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Thu, 28 Dec 2023 17:12:15 +0900 Subject: [PATCH] ColabFold v1.5.4 --- .github/workflows/docker.yml | 2 +- AlphaFold2.ipynb | 4 ++-- Dockerfile | 2 +- README.md | 2 +- batch/AlphaFold2_batch.ipynb | 4 ++-- pyproject.toml | 2 +- 6 files changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml index 80cc8bb3..059744f0 100644 --- a/.github/workflows/docker.yml +++ b/.github/workflows/docker.yml @@ -7,7 +7,7 @@ on: description: 'ColabFold Conda version' required: true type: string - default: '1.5.3' + default: '1.5.4' env: REGISTRY: ghcr.io diff --git a/AlphaFold2.ipynb b/AlphaFold2.ipynb index dc7ff151..2aec3e59 100644 --- a/AlphaFold2.ipynb +++ b/AlphaFold2.ipynb @@ -46,10 +46,10 @@ "source": [ "\n", "\n", - "##ColabFold v1.5.3: AlphaFold2 using MMseqs2\n", + "##ColabFold v1.5.4: AlphaFold2 using MMseqs2\n", "\n", "Easy to use protein structure and complex prediction using [AlphaFold2](https://www.nature.com/articles/s41586-021-03819-2) and [Alphafold2-multimer](https://www.biorxiv.org/content/10.1101/2021.10.04.463034v1). Sequence alignments/templates are generated through [MMseqs2](mmseqs.com) and [HHsearch](https://github.com/soedinglab/hh-suite). For more details, see bottom of the notebook, checkout the [ColabFold GitHub](https://github.com/sokrypton/ColabFold) and read our manuscript.\n", - "Old versions: [v1.4](https://colab.research.google.com/github/sokrypton/ColabFold/blob/v1.4.0/AlphaFold2.ipynb), [v1.5.1](https://colab.research.google.com/github/sokrypton/ColabFold/blob/v1.5.1/AlphaFold2.ipynb), [v1.5.2](https://colab.research.google.com/github/sokrypton/ColabFold/blob/v1.5.2/AlphaFold2.ipynb)\n", + "Old versions: [v1.4](https://colab.research.google.com/github/sokrypton/ColabFold/blob/v1.4.0/AlphaFold2.ipynb), [v1.5.1](https://colab.research.google.com/github/sokrypton/ColabFold/blob/v1.5.1/AlphaFold2.ipynb), [v1.5.2](https://colab.research.google.com/github/sokrypton/ColabFold/blob/v1.5.2/AlphaFold2.ipynb), [v1.5.3](https://colab.research.google.com/github/sokrypton/ColabFold/blob/v1.5.3/AlphaFold2.ipynb)\n", "\n", "[Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M. ColabFold: Making protein folding accessible to all.\n", "*Nature Methods*, 2022](https://www.nature.com/articles/s41592-022-01488-1)" diff --git a/Dockerfile b/Dockerfile index ba51eda0..1bf3a71b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,5 +1,5 @@ ARG CUDA_VERSION=11.8.0 -ARG COLABFOLD_VERSION=1.5.3 +ARG COLABFOLD_VERSION=1.5.4 FROM nvidia/cuda:${CUDA_VERSION}-base-ubuntu22.04 RUN apt-get update && apt-get install -y wget cuda-nvcc-$(echo $CUDA_VERSION | cut -d'.' -f1,2 | tr '.' '-') --no-install-recommends --no-install-suggests && rm -rf /var/lib/apt/lists/* && \ diff --git a/README.md b/README.md index 1dd79833..a90a51f3 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# ColabFold - v1.5.3 +# ColabFold - v1.5.4 For details of what was changed in v1.5, see [change log](https://github.com/sokrypton/ColabFold/wiki/v1.5.0)! diff --git a/batch/AlphaFold2_batch.ipynb b/batch/AlphaFold2_batch.ipynb index 64d67395..05b9cca2 100644 --- a/batch/AlphaFold2_batch.ipynb +++ b/batch/AlphaFold2_batch.ipynb @@ -34,7 +34,7 @@ "id": "G4yBrceuFbf3" }, "source": [ - "#ColabFold v1.5.3: AlphaFold2 w/ MMseqs2 BATCH\n", + "#ColabFold v1.5.4: AlphaFold2 w/ MMseqs2 BATCH\n", "\n", "\n", "\n", @@ -49,7 +49,7 @@ "\n", "`result_dir` results will be written to the result directory in Google Drive\n", "\n", - "Old versions: [v1.4](https://colab.research.google.com/github/sokrypton/ColabFold/blob/v1.4.0/batch/AlphaFold2_batch.ipynb), [v1.5.1](https://colab.research.google.com/github/sokrypton/ColabFold/blob/v1.5.1//batch/AlphaFold2_batch.ipynb), [v1.5.2](https://colab.research.google.com/github/sokrypton/ColabFold/blob/v1.5.2//batch/AlphaFold2_batch.ipynb)\n", + "Old versions: [v1.4](https://colab.research.google.com/github/sokrypton/ColabFold/blob/v1.4.0/batch/AlphaFold2_batch.ipynb), [v1.5.1](https://colab.research.google.com/github/sokrypton/ColabFold/blob/v1.5.1//batch/AlphaFold2_batch.ipynb), [v1.5.2](https://colab.research.google.com/github/sokrypton/ColabFold/blob/v1.5.2//batch/AlphaFold2_batch.ipynb), [v1.5.3](https://colab.research.google.com/github/sokrypton/ColabFold/blob/v1.5.3//batch/AlphaFold2_batch.ipynb)\n", "\n", "For more details, see bottom of the notebook and checkout the [ColabFold GitHub](https://github.com/sokrypton/ColabFold). \n", "\n", diff --git a/pyproject.toml b/pyproject.toml index b3f00248..5693a7a3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "colabfold" -version = "1.5.3" +version = "1.5.4" description = "Making protein folding accessible to all. Predict proteins structures both in google colab and on your machine" authors = [ "Milot Mirdita ",