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Using AlphaFold via SBGrid
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| Avertissement |
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SBGrid is a software infrastructure that includes a library of over 400 structural biology applications, including AlphaFold. The SBGrid software collection is restricted to SBGrid member laboratories. |
The current version installed on our server is Alphafold2 2.1.1 already installed on the bioinformatics infrastructure of the structural biology platform and can be accessed either remotely via SSH or physically by logging into one of the computers in room C-305 (Roger-Gaudry building). More details are given on the SBGrid Wiki page for AlphaFold.
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# Alphafold2Alphafold 2, version 2.1.1 # wrapper script to run Alphafold for a multimer # # usage: # ./run_alphafold_tempate_multimer.sh multiple_sequences.fasta # # adjust parameters as required 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="${DATA_DIR}/pdb_mmcif/mmcif_files" PDB70_DB_files" PDB70_DB="${DATA_DIR}/pdb70/pdb70" OBSOLETE_PATH="${DATA_DIR}/pdb_mmcif/obsolete.dat" PDB_SEQRES_DATABASE_PATH="${DATA_DIR}/pdb70/pdb70" OBSOLETEpdb_seqres/pdb_seqres.txt" UNIPROT_DATABASE_PATH="${DATA_DIR}/pdb_mmcifuniprot/obsoleteuniprot.datfasta" run_alphafold.py \ --data_dir=$DATA_DIR \ --output_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 \ --pdb70pdb_seqres_database_path=$PDB_SEQRES_DATABASE_PATH \ --uniprot_database_path=$PDB70$UNIPROT_DATABASE_DBPATH \ --obsolete_pdbs_path=$OBSOLETE_PATH \ --model_preset=multimer \ --fasta_paths=${1} |
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