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- A modified version of the AlphaFold wrapper provided by SBGrid that can be downloaded here.
- Your protein sequence in FASTA format (a complete description of the FAST FASTA format can be found here). The description line is mandatory. An example file can be downloaded here.
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> Rift Valley Fever Virus NSs protein MDYFPVISVDLQSGRRVVSVEYFRGDGPPRIPYSMVGPCCVFLMHHRPSHEVRLRFSDFY NVGEFPYRVGLGDFASNVAPPPAKPFQRLIDLIGHMTLSDFTRFPNLKEAISWPLGEPSL AFFDLSSTRVHRNDDIRRDQIATLAMRSCKITNDLEDSFVGLHRMIATEAILRGIDLCLL PGFDLMYEVAHVQCVRLLQAAKEDISNAVVPNSALIVLMEESLMLRSSLPSMMGRNNWIP VIPPIPDVEMESEEESDDDGFVEVD |
Then, to run AlphaFold, enter the following command in the terminal promptContent of the run_alphafold_template.sh wrapper:
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DATA_DIR="/home/sbio/afdb/" OUTPUT_DIR=$(pwd) MAX_TEMPLATE_DATE=$(date -I) DB_PRESET="full_dbs" BFD_DB="${DATA_DIR}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt" UNICLUST30_DB="${DATA_DIR}/uniclust30/uniclust30_2018_08/uniclust30_2018_08" UNIREF90_DB="${DATA_DIR}/uniref90/uniref90.fasta" MGNIFY_DB="${DATA_DIR}/mgnify/mgy_clusters_2018_12.fa" TEMPLATE_MMCIF_DIR="${DATA_DIR}/pdb_mmcif/mmcif_files" PDB70_DB="${DATA_DIR}/pdb70/pdb70" OBSOLETE_PATH="${DATA_DIR}/pdb_mmcif/obsolete.dat" run_alphafold.py \ --data_dir=$DATA_DIR \ --output_template.sh [FASTA filename] [output directory] |
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dir=$OUTPUT_DIR \
--max_template_date=$MAX_TEMPLATE_DATE \
--db_preset=$DB_PRESET \
--bfd_database_path=$BFD_DB \
--uniclust30_database_path=$UNICLUST30_DB \
--uniref90_database_path=$UNIREF90_DB \
--mgnify_database_path=$MGNIFY_DB \
--template_mmcif_dir=$TEMPLATE_MMCIF_DIR \
--pdb70_database_path=$PDB70_DB \
--obsolete_pdbs_path=$OBSOLETE_PATH \
--fasta_paths=test_monomer.fasta \ |
Make sure to replace the --fasta_paths= value to point to your FASTA file in the run_alphafold_template.sh wrapper.
Then, to run AlphaFold, enter the following command in the terminal prompt:
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./run_alphafold_template.sh NSs.fasta /home/sbio/norm/data/alphafold | ||
| Avertissement | ||
If you do not specify the output directory, it will be saved by default to /tmp/alphafold. However, the data will be deleted after 7 days, so make sure you copy it onto your local home directory. |
As a reference, it took about 60 minutes for the calculation to predict 5 models for RVFV NSs (the sequence given as example above) to take place on mazuelo. Once it is done, you can go to the results folder and analyze your results. A description of the various files produced by the program is provided on the GitHub page of AlphaFold.
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