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auto-generated MSA intergation
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‎README.md

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## License
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Our model and code are released under MIT License, and can be freely used for both academic and commercial purposes.
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## Cite
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If you use this code or the models in your research, please cite the following papers:
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```bibtex
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@article{mirdita2022colabfold,
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title={Boltz-1: Democratizing Biomolecular Interaction Modeling},
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author={Wohlwend, Jeremy and Corso, Gabriele and Passaro, Saro and Reveiz, Mateo and Leidal, Ken and Swiderski, Wojtek and Portnoi, Tally and Chinn, Itamar and Siltera, Jacob and Jaakkola, Tommi and Barzilay, Regina},
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journal={},
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year={2024},
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}
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```
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```bibtex
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@article{mirdita2022colabfold,
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title={ColabFold: making protein folding accessible to all},
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author={Mirdita, Milot and Sch{\"u}tze, Konstantin and Moriwaki, Yoshitaka and Heo, Lim and Ovchinnikov, Sergey and Steinegger, Martin},
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journal={Nature methods},
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volume={19},
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number={6},
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pages={679--682},
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year={2022},
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publisher={Nature Publishing Group US New York}
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}
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```

‎docs/prediction.md

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## Fasta format
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The fasta format should contain entries as follows:
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```
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>CHAIN_ID|ENTITY_TYPE|MSA_PATH
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SEQUENCE
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```
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The `CHAIN_ID` is a unique identifier for each input chain. The `ENTITY_TYPE` can be one of `protein`, `dna`, `rna`, `smiles`, `ccd` (note that we support both smiles and CCD code for ligands). The `MSA_PATH` is only specified for protein entities and is the path to the `.a3m` file containing a pre-computed MSA for the sequence of the protein. If you wish to explicitly run single sequence mode (which is generally advised against as it will hurt model performance), you may do so by using the special keyword `empty` for that protein (ex: `>A|protein|empty`).
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For each of these cases, the corresponding `SEQUENCE` will contain an amino acid sequence (e.g. `EFKEAFSLF`), a sequence of nucleotide bases (e.g. `ATCG`), a smiles string (e.g. `CC1=CC=CC=C1`), or a CCD code (e.g. `ATP`), depending on the entity.
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As an example:
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```yaml
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>A|protein|./examples/msa/seq1.a3m
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MVTPEGNVSLVDESLLVGVTDEDRAVRSAHQFYERLIGLWAPAVMEAAHELGVFAALAEAPADSGELARRLDCDARAMRVLLDALYAYDVIDRIHDTNGFRYLLSAEARECLLPGTLFSLVGKFMHDINVAWPAWRNLAEVVRHGARDTSGAESPNGIAQEDYESLVGGINFWAPPIVTTLSRKLRASGRSGDATASVLDVGCGTGLYSQLLLREFPRWTATGLDVERIATLANAQALRLGVEERFATRAGDFWRGGWGTGYDLVLFANIFHLQTPASAVRLMRHAAACLAPDGLVAVVDQIVDADREPKTPQDRFALLFAASMTNTGGGDAYTFQEYEEWFTAAGLQRIETLDTPMHRILLARRATEPSAVPEGQASENLYFQ
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>B|protein|./examples/msa/seq1.a3m
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MVTPEGNVSLVDESLLVGVTDEDRAVRSAHQFYERLIGLWAPAVMEAAHELGVFAALAEAPADSGELARRLDCDARAMRVLLDALYAYDVIDRIHDTNGFRYLLSAEARECLLPGTLFSLVGKFMHDINVAWPAWRNLAEVVRHGARDTSGAESPNGIAQEDYESLVGGINFWAPPIVTTLSRKLRASGRSGDATASVLDVGCGTGLYSQLLLREFPRWTATGLDVERIATLANAQALRLGVEERFATRAGDFWRGGWGTGYDLVLFANIFHLQTPASAVRLMRHAAACLAPDGLVAVVDQIVDADREPKTPQDRFALLFAASMTNTGGGDAYTFQEYEEWFTAAGLQRIETLDTPMHRILLARRATEPSAVPEGQASENLYFQ
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>C|ccd
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SAH
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>D|ccd
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SAH
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>E|smiles
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N[C@@H](Cc1ccc(O)cc1)C(=O)O
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>F|smiles
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N[C@@H](Cc1ccc(O)cc1)C(=O)O
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```
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## YAML format
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The YAML format is more flexible and allows for more complex inputs, particularly around covalent bonds. The schema of the YAML is the following:
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binder: CHAIN_ID
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contacts: [[CHAIN_ID, RES_IDX], [CHAIN_ID, RES_IDX]]
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```
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`sequences` has one entry for every unique chain/molecule in the input. Each polymer entity as a `ENTITY_TYPE` either `protein`, `dna` or`rna` and have a `sequence` attribute. Non-polymer entities are indicated by `ENTITY_TYPE` equal to `ligand` and have a `smiles` or `ccd` attribute. `CHAIN_ID` is the unique identifier for each chain/molecule, and it should be set as a list in case of multiple identical entities in the structure. Protein entities should also contain an `msa` attribute with `MSA_PATH` indicating the path to the `.a3m` file containing a computed MSA for the sequence of the protein. If you wish to explicitly run single sequence mode (which is generally advised against as it will hurt model performance), you may do so by using the special keyword `empty` for that protein (ex: `msa: empty`).
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`sequences` has one entry for every unique chain/molecule in the input. Each polymer entity as a `ENTITY_TYPE` either `protein`, `dna` or`rna` and have a `sequence` attribute. Non-polymer entities are indicated by `ENTITY_TYPE` equal to `ligand` and have a `smiles` or `ccd` attribute. `CHAIN_ID` is the unique identifier for each chain/molecule, and it should be set as a list in case of multiple identical entities in the structure. For proteins, the `msa` key is optional. If unset, MSA's will be automatically generated using the mmseqs2 server. If you wish to use a precomputed MSA, use the `msa` attribute with `MSA_PATH` indicating the path to the `.a3m` file containing the MSA for that protein. If you wish to explicitly run single sequence mode (which is generally advised against as it will hurt model performance), you may do so by using the special keyword `empty` for that protein (ex: `msa: empty`).
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The `modifications` field is an optional field that allows you to specify modified residues in the polymer (`protein`, `dna` or`rna`). The `position` field specifies the index (starting from 1) of the residue, and `ccd` is the CCD code of the modified residue. This field is currently only supported for CCD ligands.
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```
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## Fasta format
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The fasta format is a little simpler, and should contain entries as follows:
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```
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>CHAIN_ID|ENTITY_TYPE|MSA_PATH
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SEQUENCE
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```
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The `CHAIN_ID` is a unique identifier for each input chain. The `ENTITY_TYPE` can be one of `protein`, `dna`, `rna`, `smiles`, `ccd` (note that we support both smiles and CCD code for ligands). The `MSA_PATH` is optional, and only applicable to proteins. By default, MSA's are auto-generated using the mmseqs2 server. If you wish to use a custom MSA, use it toset path to the `.a3m` file containing a pre-computed MSA for this protein. If you wish to explicitly run single sequence mode (which is generally advised against as it will hurt model performance), you may do so by using the special keyword `empty` for that protein (ex: `>A|protein|empty`).
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For each of these cases, the corresponding `SEQUENCE` will contain an amino acid sequence (e.g. `EFKEAFSLF`), a sequence of nucleotide bases (e.g. `ATCG`), a smiles string (e.g. `CC1=CC=CC=C1`), or a CCD code (e.g. `ATP`), depending on the entity.
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As an example:
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```yaml
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>A|protein|./examples/msa/seq1.a3m
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MVTPEGNVSLVDESLLVGVTDEDRAVRSAHQFYERLIGLWAPAVMEAAHELGVFAALAEAPADSGELARRLDCDARAMRVLLDALYAYDVIDRIHDTNGFRYLLSAEARECLLPGTLFSLVGKFMHDINVAWPAWRNLAEVVRHGARDTSGAESPNGIAQEDYESLVGGINFWAPPIVTTLSRKLRASGRSGDATASVLDVGCGTGLYSQLLLREFPRWTATGLDVERIATLANAQALRLGVEERFATRAGDFWRGGWGTGYDLVLFANIFHLQTPASAVRLMRHAAACLAPDGLVAVVDQIVDADREPKTPQDRFALLFAASMTNTGGGDAYTFQEYEEWFTAAGLQRIETLDTPMHRILLARRATEPSAVPEGQASENLYFQ
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>B|protein|./examples/msa/seq1.a3m
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MVTPEGNVSLVDESLLVGVTDEDRAVRSAHQFYERLIGLWAPAVMEAAHELGVFAALAEAPADSGELARRLDCDARAMRVLLDALYAYDVIDRIHDTNGFRYLLSAEARECLLPGTLFSLVGKFMHDINVAWPAWRNLAEVVRHGARDTSGAESPNGIAQEDYESLVGGINFWAPPIVTTLSRKLRASGRSGDATASVLDVGCGTGLYSQLLLREFPRWTATGLDVERIATLANAQALRLGVEERFATRAGDFWRGGWGTGYDLVLFANIFHLQTPASAVRLMRHAAACLAPDGLVAVVDQIVDADREPKTPQDRFALLFAASMTNTGGGDAYTFQEYEEWFTAAGLQRIETLDTPMHRILLARRATEPSAVPEGQASENLYFQ
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>C|ccd
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SAH
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>D|ccd
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SAH
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>E|smiles
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N[C@@H](Cc1ccc(O)cc1)C(=O)O
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>F|smiles
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N[C@@H](Cc1ccc(O)cc1)C(=O)O
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```
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## Options
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The following options are available for the `predict` command:

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