AlphaFold

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Description

This package provides an implementation of the inference pipeline of AlphaFold v2.0. 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. https://github.com/deepmind/alphafold

Availability

Application is prepared as singularity image and downloaded datasets with example scripts to run with PBS in Metacentrum modules. Location:

  • Location: /storage/brno11-elixir/projects/alphafold

Use

Three different example script with control of AlphaFold speed / quality tradeoff by adding --preset=reduced_dbs, --preset=full_dbs or --preset=casp14 to the run command. We provide the following presets:

  • reduced_dbs_regular_run.sh - reduced_dbs: This preset is optimized for speed and lower hardware requirements. It runs with a reduced version of the BFD database and with no ensembling. It requires 8 CPU cores (vCPUs), 8 GB of RAM, and 600 GB of disk space.
  • full_dbs_regular_run.sh - full_dbs: The model in this preset is 8 times faster than the casp14 preset with a very minor quality drop (-0.1 average GDT drop on CASP14 domains). It runs with all genetic databases and with no ensembling.
  • casp14_regular_run.sh - casp14: This preset uses the same settings as were used in CASP14. It runs with all genetic databases and with 8 ensemblings.


Documentation

URL: https://github.com/deepmind/alphafold

Licence

https://github.com/deepmind/alphafold#license-and-disclaimer

Program administrator

meta@cesnet.cz

Homepage

URL: https://github.com/deepmind/alphafold

Tips and useful information

Example of run with different --preset with example file test.fasta. This test shows difference of RAM consuming a length of run with the same test. More results will be added/updated.

--preset cluster / RAM Duration
casp14 zia / 221 GB 52 min
full-dbs adan / 160 GB 55 min
reduced_dbs zia / 153 GB 52 min

Example of run with different --preset with example file covidGB.fasta. The jobs are runnig right now :-)

--preset cluster / RAM Duration
casp14 zia / xxx GB xx min
full-dbs zia / xxx GB xx min
reduced_dbs zia / xxx GB xx min

Useful links