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basic usage.md

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AlphaFold Basic Usage

Run prediction

Monomer

  1. start a new tmux session with

    tmux new -s session_name

    This starts a named tmux session that runs even after you turn off laptop (as long as instance is still running on AWS).

  2. Cd into efs volume (or whichever folder you want to save your results)

    cd /efs

  3. Optionally, I make a folder specific to my project, for example:

    mkdir myproject

  4. Copy paste sequence into the a fasta file

    cd myproject
vim myfasta.fasta

    For example:

    >myseq
PUTSEQUENCEHERE

  5. Make sure you in tmux mode. Then activate environment

    source activate alphafold

  6. Run

    python3 /data/alphafold/docker/run_docker.py --fasta_paths=/efs/myproject/myfasta.fasta --output_dir=/efs/myproject --model_preset=monomer

Heterodimer

Similar to homodimers, except you put the 2 sequences in 1 fasta file.

  1. For example:

    >chain1
CHAINSEQUENCE

>chain2
CHAINSEQUENCE

  2. Activate env by source activate alphafold. Then Run the multimer mode:

    python3 /data/alphafold/docker/run_docker.py --fasta_paths=/efs/myproject/myfasta.fasta --output_dir=/efs/myproject --model_preset=multimer

Homomer (General)

Method is similar, but in the fasta file provide N copies of the same sequence. For example, if the homomer has 3 copies of the same sequence, your input fasta file should be:

>sequence_1
<SEQUENCE>
>sequence_2
<SEQUENCE>
>sequence_3
<SEQUENCE>

Run command is same as heterodimer.

Heteromer (General)

Say we have an A2B3 heteromer, i.e. with 2 copies of <SEQUENCE A> and 3 copies of <SEQUENCE B>. The input fasta should be:

>sequence_1
<SEQUENCE A>
>sequence_2
<SEQUENCE A>
>sequence_3
<SEQUENCE B>
>sequence_4
<SEQUENCE B>
>sequence_5
<SEQUENCE B>

Run command is same as heterodimer.

Multiple fasta files

Similar as described before, just pass this argument:

For example:

--fasta_paths=multimer1.fasta,multimer2.fasta