Introduction
AlphaFold is an artificial intelligence based software developed by DeepMind Technologies, a subsidiary of Alphabet (parent company of Google) which performs protein structure prediction using a deep learning system. Initial demonstration of the program at CASP13 showed great success at accurately predicting structures for targets rated as being the most difficult, where no previous template existed. In a second public demonstration during the 14th CASP in 2020, the AlphaFold team achieved a level of accuracy much higher than any other participating group.
Such results have proven to be a giant step forward in the field of ab initio protein structure prediction. Later in July 2021, DeepMind published a paper in Nature describing AlphaFold. It also made public the source code of the software on GitHub and offered a searchable database containing the structure prediction result of the complete proteome of about 20 species (over 365 000 protein structures).
How AlphaFold works
Using AlphaFold via SBGrid
SBGrid is a software infrastructure that includes a library of over 400 structural biology applications, including AlphaFold. The SBGrid software collection is 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.
A username and password are required to access the infrastructure. They can be requested by email to Normand Cyr or Ryan Richter.
Once logged in, open a terminal window and on the command prompt, type
sbgrid
This will activate the SBGrid environment and allow you to access the various applications. You should see the following welcome message
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Software Support by SBGrid (www.sbgrid.org)
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Your use of the applications contained in the /programs directory constitutes
acceptance of the terms of the SBGrid License Agreement included in the file
/programs/share/LICENSE. The applications distributed by SBGrid are licensed
exclusively to member laboratories of the SBGrid Consortium.
Run sbgrid-accept-license to remove the above message.
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SBGrid was developed with support from its members, Harvard Medical School,
HHMI, and NSF. If use of SBGrid compiled software was an important element
in your publication, please include the following reference in your work:
Software used in the project was installed and configured by SBGrid.
cite: eLife 2013;2:e01456, Collaboration gets the most out of software.
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SBGrid installation last updated: 2021-07-25
Please submit bug reports and help requests to: <bugs@sbgrid.org> or
<http://sbgrid.org/bugs>
For additional information visit https://sbgrid.org/wiki
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If you do not activate the SBGrid environment, you will get the following error message
SBGrid shell environment is not initialized! Please source /programs/sbgrid.shrc or /programs/sbgrid.cshrc to use the software.
In order to run AlphaFold, you will need at least two text files:
- A modified version of the AlphaFold wrapper provided by SBGrid that can be downloaded here.
- Your protein sequence in FASTA format. The description line is mandatory. An example file can be downloaded here.
Example FASTA file:
> Rift Valley Fever Virus NSs protein MDYFPVISVDLQSGRRVVSVEYFRGDGPPRIPYSMVGPCCVFLMHHRPSHEVRLRFSDFY NVGEFPYRVGLGDFASNVAPPPAKPFQRLIDLIGHMTLSDFTRFPNLKEAISWPLGEPSL AFFDLSSTRVHRNDDIRRDQIATLAMRSCKITNDLEDSFVGLHRMIATEAILRGIDLCLL PGFDLMYEVAHVQCVRLLQAAKEDISNAVVPNSALIVLMEESLMLRSSLPSMMGRNNWIP VIPPIPDVEMESEEESDDDGFVEVD
Then, to run AlphaFold, enter the following command in the terminal prompt:
./run_alphafold_template.sh [FASTA filename] [output directory]
For example, with the FASTA file presented above:
./run_alphafold_template.sh NSs.fasta /home/sbio/norm/data/alphafold
If you do not specify the output directory, it will be saved, by default to /tmp/alphafold. However, the data will be deleted after 7 days, so make sure you copy it onto your local home directory.