78 lines
3.2 KiB
Markdown
78 lines
3.2 KiB
Markdown
# Multimer Inference
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To run inference on a complex or multiple complexes using a set of DeepMind's pretrained parameters, you will need:
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- AlphaFold Multimer v2.3 parameters
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- Updated sequence databases, with UniRef and PDB Seqres databases.
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## Upgrade from a previous OpenFold Installation
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If you had previously downloaded OpenFold parameters and or AlphaFold databases, you will need to download updated versions. Here are some instructions for upgrading from an existing openfold installations.
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### Download AlphaFold-Multimer v2.3 Model Parameters
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1. Re-download the alphafold parameters to get the latest
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AlphaFold-Multimer v2.3 weights:
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```bash
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bash scripts/download_alphafold_params.sh openfold/resources
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```
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### Download AlphaFold Databases for Multimer
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1. Download the [UniProt](https://www.uniprot.org/uniprotkb/)
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and [PDB SeqRes](https://www.rcsb.org/) databases:
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```bash
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bash scripts/download_uniprot.sh data/
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```
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The PDB SeqRes and PDB databases must be from the same date to avoid potential
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errors during template searching. Remove the existing `data/pdb_mmcif` directory
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and download both databases:
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```bash
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bash scripts/download_pdb_mmcif.sh data/
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bash scripts/download_pdb_seqres.sh data/
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```
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1. Additionally, AlphaFold-Multimer uses upgraded versions of the [MGnify](https://www.ebi.ac.uk/metagenomics)
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and [UniRef30](https://uniclust.mmseqs.com/) (previously UniClust30) databases. To download the upgraded databases, run:
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```bash
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bash scripts/download_uniref30.sh data/
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bash scripts/download_mgnify.sh data/
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```
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```{note}
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Multimer inference can also run with the older database versions if desired.
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```
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## Running Multimer Inference
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The [`run_pretrained_openfold.py`](https://github.com/aqlaboratory/openfold/blob/main/run_pretrained_openfold.py) script can be used to run multimer inference with the follwoing command.
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```bash
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python3 run_pretrained_openfold.py \
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fasta_dir \
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data/pdb_mmcif/mmcif_files/ \
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--uniref90_database_path data/uniref90/uniref90.fasta \
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--mgnify_database_path data/mgnify/mgy_clusters_2022_05.fa \
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--pdb_seqres_database_path data/pdb_seqres/pdb_seqres.txt \
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--uniref30_database_path data/uniref30/UniRef30_2021_03 \
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--uniprot_database_path data/uniprot/uniprot.fasta \
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--bfd_database_path data/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
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--jackhmmer_binary_path lib/conda/envs/openfold_venv/bin/jackhmmer \
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--hhblits_binary_path lib/conda/envs/openfold_venv/bin/hhblits \
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--hmmsearch_binary_path lib/conda/envs/openfold_venv/bin/hmmsearch \
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--hmmbuild_binary_path lib/conda/envs/openfold_venv/bin/hmmbuild \
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--kalign_binary_path lib/conda/envs/openfold_venv/bin/kalign \
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--config_preset "model_1_multimer_v3" \
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--model_device "cuda:0" \
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--output_dir ./
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```
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**Notes:**
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- Template searching in the multimer pipeline uses HMMSearch with the PDB SeqRes database, replacing HHSearch and PDB70 used in the monomer pipeline.
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- As with monomer inference, if you've already computed alignments for the query, you can use the `--use_precomputed_alignments` option.
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- At this time, only AlphaFold parameter weights are available for multimer mode. |