All steps are the same as when running the monomer system, but you will have to
* provide an input fasta with multiple sequences,
* set `--model_preset=multimer`,
* optionally set the `--is_prokaryote_list` flag with booleans that determine
whether all input sequences in the given fasta file are prokaryotic. If that
is not the case or the origin is unknown, set to `false` for that fasta.
An example that folds two protein complexes `multimer1` and `multimer2` where
the first is prokaryotic and the second isn't:
```bash
python3 docker/run_docker.py \
--fasta_paths=multimer1.fasta,multimer2.fasta \
--is_prokaryote_list=true,false \
--max_template_date=2020-05-14 \
--model_preset=multimer \
--data_dir=$DOWNLOAD_DIR
```
### AlphaFold output
### AlphaFold output
The outputs will be in a subfolder of `output_dir` in `run_docker.py`. They
The outputs will be saved in a subdirectory of the directory provided via the
include the computed MSAs, unrelaxed structures, relaxed structures, ranked
`--output_dir` flag of `run_docker.py` (defaults to `/tmp/alphafold/`). The
structures, raw model outputs, prediction metadata, and section timings. The
outputs include the computed MSAs, unrelaxed structures, relaxed structures,
`output_dir` directory will have the following structure:
ranked structures, raw model outputs, prediction metadata, and section timings.
The `--output_dir` directory will have the following structure:
```
```
<target_name>/
<target_name>/
...
@@ -299,7 +406,7 @@ develop on top of the `RunModel.predict` method with a parallel system for
...
@@ -299,7 +406,7 @@ develop on top of the `RunModel.predict` method with a parallel system for
precomputing multi-sequence alignments. Alternatively, this script can be run
precomputing multi-sequence alignments. Alternatively, this script can be run
repeatedly with only moderate overhead.
repeatedly with only moderate overhead.
## Note on reproducibility
## Note on CASP14 reproducibility
AlphaFold's output for a small number of proteins has high inter-run variance,
AlphaFold's output for a small number of proteins has high inter-run variance,
and may be affected by changes in the input data. The CASP14 target T1064 is a
and may be affected by changes in the input data. The CASP14 target T1064 is a
...
@@ -346,6 +453,21 @@ If you use the code or data in this package, please cite:
...
@@ -346,6 +453,21 @@ If you use the code or data in this package, please cite:
}
}
```
```
In addition, if you use the AlphaFold-Multimer mode, please cite:
```bibtex
@article{AlphaFold-Multimer2021,
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},
