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Update alphafold.md
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lauraluebbert authored Mar 7, 2024
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Predict the 3D structure of a protein from its amino acid sequence using a simplified version of [DeepMind](https://www.deepmind.com/)’s [AlphaFold2](https://github.com/deepmind/alphafold) originally released and benchmarked for [AlphaFold Colab](https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb).
Returns: Predicted structure (PDB) and alignment error (json).

Before using `gget alphafold` for the first time, run `gget setup alphafold` / `gget.setup("alphafold")` once (also see [`gget setup`](setup.md)). Running `gget setup alphafold` / `gget.setup("alphafold")` will download and install the latest version of AlphaFold2 hosted on the [AlphaFold GitHub Repo](https://github.com/deepmind/alphafold). You can rerun this command any time to update the software after a new AlphaFold release.
Before using `gget alphafold` for the first time:
1. Install the third-party dependency openmm v7.5.1 (or v7.7.0 for Python >= 3.10) by running the following command from the command line: `conda install -qy conda==4.13.0 && conda install -qy -c conda-forge openmm=7.5.1` (or `openmm=7.7.0` for Python >= 3.10). (Recommendation: Follow with 'conda update -qy conda' to update conda to the latest version afterwards.)
2. Run `gget setup alphafold` / `gget.setup("alphafold")` once (also see [`gget setup`](setup.md)). Running `gget setup alphafold` / `gget.setup("alphafold")` will download and install the latest version of AlphaFold2 hosted on the [AlphaFold GitHub Repo](https://github.com/deepmind/alphafold). You can rerun this command any time to update the software after a new AlphaFold release.

**Positional argument**
`sequence`
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