examples/alphafold2.md
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@@ -145,6 +145,35 @@ Some command line flags have changed since version 2.0.0. We recommend running t
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### Examples
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+
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+**Alphafold2 2.3.1**
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+```
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+/programs/x86_64-linux/alphafold/${ALPHAFOLD_X}/bin.capsules/run_alphafold.py \
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+ --data_dir=/programs/local/alphafold/ \
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+ --output_dir=$(pwd) \
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+ --fasta_paths=${input} \
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+ --max_template_date=2020-05-14 \
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+ --db_preset=full_dbs \
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+ --bfd_database_path=/programs/local/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
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+ --uniref30_database_path=/programs/local/alphafold/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
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+ --uniref90_database_path=/programs/local/alphafold/uniref90/uniref90.fasta \
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+ --mgnify_database_path=/programs/local/alphafold/mgnify/mgy_clusters_2018_12.fa \
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+ --template_mmcif_dir=/programs/local/alphafold/pdb_mmcif/mmcif_files \
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+ --obsolete_pdbs_path=/programs/local/alphafold/pdb_mmcif/obsolete.dat \
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+ --use_gpu_relax=True \
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+ --model_preset=monomer \
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+ --pdb70_database_path=/programs/local/alphafold/pdb70/pdb70
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+```
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+
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+where the input fasta is
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+
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+```
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+>T1083
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+GAMGSEIEHIEEAIANAKTKADHERLVAHYEEEAKRLEKKSEEYQELAKVYKKITDVYPNIRSYMVLHYQNLTRRYKEAAEENRALAKLHHELAIVED
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+```
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+
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+This is very similar to earlier 2.2.x releases, but the `--unicluster30_database_path` has been renamed to ` --uniref30_database_path`.
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+
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**NOTE : Alphafold2 introduced new flags for GPU-based relaxation that must be specifed**.
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You can also resume from a previously run MSA. See [the alphafold2 github repo](https://github.com/deepmind/alphafold/releases/tag/v2.1.2) for more info.
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