examples/alphafold2.md
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Some command line flags have changed since version 2.0.0. We recommend running the `run_alphafold.py` command directly and are not providing a wrapper script ( as we did for 2.0.0) at the present time.
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### Examples
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+**Alphafold2 2.3.2**
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+We have example scripts available to run alphafold2 monomer and multimer in SBGrid. For a multimer example, see
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+ [alphafold_multimer.sh](alphafold_multimer.sh)
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+For monomeric single-chain predictions, use:
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+ [alphafold_monomer.sh](alphafold_multimer.sh)
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+For reference, we have [pasb_dimer.fasta](pasb_dimer.fasta) and [pasb_monomer.fasta](pasb_monomer.fasta) sequences. Use these for multimer and momomer respectively.
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**Alphafold2 2.3.1**
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```
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/programs/x86_64-linux/alphafold/${ALPHAFOLD_X}/bin.capsules/run_alphafold.py \
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This is very similar to earlier 2.2.x releases, but the `--unicluster30_database_path` has been renamed to ` --uniref30_database_path`.
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-**NOTE : Alphafold2 introduced new flags for GPU-based relaxation that must be specifed**.
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+**NOTE : Alphafold2 introduced new flags for GPU-based relaxation that must be specified**.
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You can also resume from a previously run MSA. See [the alphafold2 github repo](https://github.com/deepmind/alphafold/releases/tag/v2.1.2) for more info.
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**Alphafold2 2.1.2**