knox / AlphaFold-readme-17.sh
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| 1 | python3 docker/run_docker.py \ |
| 2 | --fasta_paths=homomer.fasta \ |
| 3 | --max_template_date=2021-11-01 \ |
| 4 | --model_preset=multimer \ |
| 5 | --data_dir=$DOWNLOAD_DIR \ |
| 6 | --output_dir=/home/user/absolute_path_to_the_output_dir |
knox / AlphaFold-readme-16.fa
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| 1 | >sequence_1 |
| 2 | <SEQUENCE> |
| 3 | >sequence_2 |
| 4 | <SEQUENCE> |
| 5 | >sequence_3 |
| 6 | <SEQUENCE> |
knox / AlphaFold-readme-15.sh
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| 1 | python3 docker/run_docker.py \ |
| 2 | --fasta_paths=monomer.fasta \ |
| 3 | --max_template_date=2021-11-01 \ |
| 4 | --model_preset=monomer \ |
| 5 | --data_dir=$DOWNLOAD_DIR \ |
| 6 | --output_dir=/home/user/absolute_path_to_the_output_dir |
knox / AlphaFold-readme-14.fa
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| 1 | >sequence_name |
| 2 | <SEQUENCE> |
knox / AlphaFold-readme-13.md
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| No. residues | Prediction time (s) |
|---|---|
| 100 | 4.9 |
| 200 | 7.7 |
| 300 | 13 |
| 400 | 18 |
| 500 | 29 |
| 600 | 36 |
| 700 | 53 |
| 800 | 60 |
knox / AlphaFold-readme-12.sh
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| 1 | python3 docker/run_docker.py \ |
| 2 | --fasta_paths=multimer.fasta \ |
| 3 | --max_template_date=2020-05-14 \ |
| 4 | --model_preset=multimer \ |
| 5 | --data_dir=$DOWNLOAD_DIR \ |
| 6 | --output_dir=/home/user/absolute_path_to_the_output_dir |
knox / AlphaFold-readme-11.sh
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| 1 | python3 docker/run_docker.py \ |
| 2 | --fasta_paths=T1050.fasta \ |
| 3 | --max_template_date=2020-05-14 \ |
| 4 | --model_preset=monomer \ |
| 5 | --db_preset=reduced_dbs \ |
| 6 | --data_dir=$DOWNLOAD_DIR \ |
| 7 | --output_dir=/home/user/absolute_path_to_the_output_dir |
knox / AlphaFold-readme-10.sh
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| 1 | $DOWNLOAD_DIR/ # Total: ~ 2.62 TB (download: 556 GB) |
| 2 | bfd/ # ~ 1.8 TB (download: 271.6 GB) |
| 3 | # 6 files. |
| 4 | mgnify/ # ~ 120 GB (download: 67 GB) |
| 5 | mgy_clusters_2022_05.fa |
| 6 | params/ # ~ 5.3 GB (download: 5.3 GB) |
| 7 | # 5 CASP14 models, |
| 8 | # 5 pTM models, |
| 9 | # 5 AlphaFold-Multimer models, |
| 10 | # LICENSE, |
knox / AlphaFold-readme-9.sh
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| 1 | scripts/download_all_data.sh <DOWNLOAD_DIR> reduced_dbs |
knox / AlphaFold-readme-8.sh
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| 1 | scripts/download_all_data.sh <DOWNLOAD_DIR> |