AlphaFold: Difference between revisions
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
This package provides an implementation of the inference pipeline of AlphaFold v2. | This package provides an implementation of the inference pipeline of AlphaFold v2.3. This is a completely new model that was entered in CASP14 and published in Nature. For simplicity, we refer to this model as AlphaFold throughout the rest of this document. | ||
<!--Modules--> | <!--Modules--> | ||
==Environment Modules== | ==Environment Modules== | ||
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
<!--Configuration--> | <!--Configuration--> | ||
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Note that Alphafold has large memory requirements and some of its stages use 4 or 8 CPUs in addition to a GPU. An example job script for a run with the test data included with the software is shown below. | Note that Alphafold has large memory requirements and some of its stages use 4 or 8 CPUs in addition to a GPU. An example job script for a run with the test data included with the software is shown below. | ||
<div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;"> | |||
'' | ''Expand this section to view sample script for version 2.1.2.'' | ||
<div class="mw-collapsible-content" style="padding: 5px;"> | |||
<pre> | <pre> | ||
#!/bin/bash | #!/bin/bash | ||
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date | date | ||
</pre> | </pre> | ||
</div> | |||
</div> | |||
'' | <div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;"> | ||
''Expand this section to view sample script for version 2.3.1.'' | |||
<div class="mw-collapsible-content" style="padding: 5px;"> | |||
<pre> | <pre> | ||
#!/bin/bash | #!/bin/bash | ||
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module load alphafold | module load alphafold | ||
alphafold_full_db.sh --fasta_paths=${HPC_ALPHAFOLD_REF}/test.fasta --output_dir=~/scratch --max_template_date=2020-05-14 --use_gpu_relax=1 | |||
date | date | ||
</pre> | </pre> | ||
</div> | |||
</div> | |||
|}} | |}} | ||
<!--Job Scripts--> | <!--Job Scripts--> | ||
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{{#if: {{#var: policy}}|==Usage Example== | {{#if: {{#var: policy}}|==Usage Example== | ||
To simplify the usage use the ' | To simplify the usage use the 'alphafold_full_db.sh' script. Simple run example: | ||
alphafold_full_db.sh --fasta_paths=${HPC_ALPHAFOLD_REF}/test.fasta --output_dir=~/scratch --max_template_date=2020-05-14 --use_gpu_relax=1 | |||
From version 2.3, the AlphaFold documentation recommends running as Docker container. However, Docker is not compatible with the HPC. AlphaFold has been installed as an apptainer container and | |||
the alphafold_full_db.sh wrapper script has been created to mimic the behavior of docker/run_docker.py as referenced in the AlphaFold documentation. alphafold_full_db,sh will specify the database location options required by alphafold. | |||
To specify these options manually, use run_alphafold.sh instead. | |||
If using the --model_preset=multimer option, use the alphafold_multimer_db.sh launch script instead. Example: | |||
alphafold_multimer_db.sh --model_preset=multimer --fasta_paths=${HPC_ALPHAFOLD_REF}/test.fasta --output_dir=~/scratch --max_template_date=2020-05-14 --use_gpu_relax=1 | |||
|}} | |}} | ||
<!--Performance--> | <!--Performance--> | ||
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{{#if: {{#var: citation}}|==Citation== | {{#if: {{#var: citation}}|==Citation== | ||
If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
<div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;"> | |||
''Expand this section to view citation instructions.'' | |||
<div class="mw-collapsible-content" style="padding: 5px;"> | |||
@Article{AlphaFold2021, | @Article{AlphaFold2021, | ||
author = Jumper, John and Evans, Richard and Pritzel, Alexander and Green, Tim and Figurnov, Michael and Ronneberger, Olaf | author = Jumper, John and Evans, Richard and Pritzel, Alexander and Green, Tim and Figurnov, Michael and Ronneberger, Olaf | ||
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https://www.nature.com/articles/s41586-021-03819-2 | https://www.nature.com/articles/s41586-021-03819-2 | ||
</div> | |||
</div> | |||
<!--Installation--> | <!--Installation--> | ||
Latest revision as of 15:38, 2 February 2024
Description
This package provides an implementation of the inference pipeline of AlphaFold v2.3. This is a completely new model that was entered in CASP14 and published in Nature. For simplicity, we refer to this model as AlphaFold throughout the rest of this document.
Environment Modules
Run module spider alphafold to find out what environment modules are available for this application.
Additional Information
Note that Alphafold has large memory requirements and some of its stages use 4 or 8 CPUs in addition to a GPU. An example job script for a run with the test data included with the software is shown below.
Expand this section to view sample script for version 2.1.2.
Expand this section to view sample script for version 2.3.1.
Usage Example
To simplify the usage use the 'alphafold_full_db.sh' script. Simple run example:
alphafold_full_db.sh --fasta_paths=${HPC_ALPHAFOLD_REF}/test.fasta --output_dir=~/scratch --max_template_date=2020-05-14 --use_gpu_relax=1
From version 2.3, the AlphaFold documentation recommends running as Docker container. However, Docker is not compatible with the HPC. AlphaFold has been installed as an apptainer container and the alphafold_full_db.sh wrapper script has been created to mimic the behavior of docker/run_docker.py as referenced in the AlphaFold documentation. alphafold_full_db,sh will specify the database location options required by alphafold.
To specify these options manually, use run_alphafold.sh instead.
If using the --model_preset=multimer option, use the alphafold_multimer_db.sh launch script instead. Example:
alphafold_multimer_db.sh --model_preset=multimer --fasta_paths=${HPC_ALPHAFOLD_REF}/test.fasta --output_dir=~/scratch --max_template_date=2020-05-14 --use_gpu_relax=1
Citation
If you publish research that uses alphafold you have to cite it as follows:
Expand this section to view citation instructions.