knox / Typesense-readme-3.py
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| 1 | import typesense |
| 2 | |
| 3 | client = typesense.Client({ |
| 4 | 'api_key': 'Hu52dwsas2AdxdE', |
| 5 | 'nodes': [{ |
| 6 | 'host': 'localhost', |
| 7 | 'port': '8108', |
| 8 | 'protocol': 'http' |
| 9 | }], |
| 10 | 'connection_timeout_seconds': 2 |
knox / Typesense-readme-2.sh
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| 1 | pip install typesense |
knox / Typesense-readme-1.sh
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| 1 | docker run -p 8108:8108 -v/tmp/data:/data typesense/typesense:27.1 --data-dir /data --api-key=Hu52dwsas2AdxdE |
knox / AlphaFold-readme-24.bibtex
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| 1 | @article {AlphaFold-Multimer2021, |
| 2 | author = {Evans, Richard and O{\textquoteright}Neill, Michael and Pritzel, Alexander and Antropova, Natasha and Senior, Andrew and Green, Tim and {\v{Z}}{\'\i}dek, Augustin and Bates, Russ and Blackwell, Sam and Yim, Jason and Ronneberger, Olaf and Bodenstein, Sebastian and Zielinski, Michal and Bridgland, Alex and Potapenko, Anna and Cowie, Andrew and Tunyasuvunakool, Kathryn and Jain, Rishub and Clancy, Ellen and Kohli, Pushmeet and Jumper, John and Hassabis, Demis}, |
| 3 | journal = {bioRxiv}, |
| 4 | title = {Protein complex prediction with AlphaFold-Multimer}, |
| 5 | year = {2021}, |
| 6 | elocation-id = {2021.10.04.463034}, |
| 7 | doi = {10.1101/2021.10.04.463034}, |
| 8 | URL = {https://www.biorxiv.org/content/early/2021/10/04/2021.10.04.463034}, |
| 9 | eprint = {https://www.biorxiv.org/content/early/2021/10/04/2021.10.04.463034.full.pdf}, |
| 10 | } |
knox / AlphaFold-readme-23.bibtex
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| 1 | @Article{AlphaFold2021, |
| 2 | author = {Jumper, John and Evans, Richard and Pritzel, Alexander and Green, Tim and Figurnov, Michael and Ronneberger, Olaf and Tunyasuvunakool, Kathryn and Bates, Russ and {\v{Z}}{\'\i}dek, Augustin and Potapenko, Anna and Bridgland, Alex and Meyer, Clemens and Kohl, Simon A A and Ballard, Andrew J and Cowie, Andrew and Romera-Paredes, Bernardino and Nikolov, Stanislav and Jain, Rishub and Adler, Jonas and Back, Trevor and Petersen, Stig and Reiman, David and Clancy, Ellen and Zielinski, Michal and Steinegger, Martin and Pacholska, Michalina and Berghammer, Tamas and Bodenstein, Sebastian and Silver, David and Vinyals, Oriol and Senior, Andrew W and Kavukcuoglu, Koray and Kohli, Pushmeet and Hassabis, Demis}, |
| 3 | journal = {Nature}, |
| 4 | title = {Highly accurate protein structure prediction with {AlphaFold}}, |
| 5 | year = {2021}, |
| 6 | volume = {596}, |
| 7 | number = {7873}, |
| 8 | pages = {583--589}, |
| 9 | doi = {10.1038/s41586-021-03819-2} |
| 10 | } |
knox / AlphaFold-readme-22.sh
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| 1 | <target_name>/ |
| 2 | features.pkl |
| 3 | ranked_{0,1,2,3,4}.pdb |
| 4 | ranking_debug.json |
| 5 | relax_metrics.json |
| 6 | relaxed_model_{1,2,3,4,5}.pdb |
| 7 | result_model_{1,2,3,4,5}.pkl |
| 8 | timings.json |
| 9 | unrelaxed_model_{1,2,3,4,5}.pdb |
| 10 | msas/ |
knox / AlphaFold-readme-21.sh
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| 1 | python3 docker/run_docker.py \ |
| 2 | --fasta_paths=multimer1.fasta,multimer2.fasta \ |
| 3 | --max_template_date=2021-11-01 \ |
| 4 | --model_preset=multimer \ |
| 5 | --data_dir=$DOWNLOAD_DIR \ |
| 6 | --output_dir=/home/user/absolute_path_to_the_output_dir |
knox / AlphaFold-readme-20.sh
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| 1 | python3 docker/run_docker.py \ |
| 2 | --fasta_paths=monomer1.fasta,monomer2.fasta \ |
| 3 | --max_template_date=2021-11-01 \ |
| 4 | --model_preset=monomer \ |
| 5 | --data_dir=$DOWNLOAD_DIR \ |
| 6 | --output_dir=/home/user/absolute_path_to_the_output_dir |
knox / AlphaFold-readme-19.sh
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| 1 | python3 docker/run_docker.py \ |
| 2 | --fasta_paths=heteromer.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 |