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21 changes: 21 additions & 0 deletions ProteinMPNN/LICENSE
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MIT License

Copyright (c) 2022 Justas Dauparas

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
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The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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106 changes: 106 additions & 0 deletions ProteinMPNN/README.md
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# ProteinMPNN
![ProteinMPNN](https://docs.google.com/drawings/d/e/2PACX-1vTtnMBDOq8TpHIctUfGN8Vl32x5ISNcPKlxjcQJF2q70PlaH2uFlj2Ac4s3khnZqG1YxppdMr0iTyk-/pub?w=889&h=358)
Read [ProteinMPNN paper](https://www.biorxiv.org/content/10.1101/2022.06.03.494563v1).

To run ProteinMPNN clone this github repo and install Python>=3.0, PyTorch, Numpy.

Full protein backbone models: `vanilla_model_weights/v_48_002.pt, v_48_010.pt, v_48_020.pt, v_48_030.pt`.

CA only models: `ca_model_weights/v_48_002.pt, v_48_010.pt, v_48_020.pt`. Enable flag `--ca_only` to use these models.

Helper scripts: `helper_scripts` - helper functions to parse PDBs, assign which chains to design, which residues to fix, adding AA bias, tying residues etc.

Code organization:
* `protein_mpnn_run.py` - the main script to initialialize and run the model.
* `protein_mpnn_utils.py` - utility functions for the main script.
* `examples/` - simple code examples.
* `inputs/` - input PDB files for examples
* `outputs/` - outputs from examples
* `colab_notebooks/` - Google Colab examples
* `training/` - code and data to retrain the model
-----------------------------------------------------------------------------------------------------
Input flags for `protein_mpnn_run.py`:
```
argparser.add_argument("--ca_only", action="store_true", default=False, help="Parse CA-only structures and use CA-only models (default: false)")
argparser.add_argument("--path_to_model_weights", type=str, default="", help="Path to model weights folder;")
argparser.add_argument("--model_name", type=str, default="v_48_020", help="ProteinMPNN model name: v_48_002, v_48_010, v_48_020, v_48_030; v_48_010=version with 48 edges 0.10A noise")
argparser.add_argument("--seed", type=int, default=0, help="If set to 0 then a random seed will be picked;")
argparser.add_argument("--save_score", type=int, default=0, help="0 for False, 1 for True; save score=-log_prob to npy files")
argparser.add_argument("--save_probs", type=int, default=0, help="0 for False, 1 for True; save MPNN predicted probabilites per position")
argparser.add_argument("--score_only", type=int, default=0, help="0 for False, 1 for True; score input backbone-sequence pairs")
argparser.add_argument("--conditional_probs_only", type=int, default=0, help="0 for False, 1 for True; output conditional probabilities p(s_i given the rest of the sequence and backbone)")
argparser.add_argument("--conditional_probs_only_backbone", type=int, default=0, help="0 for False, 1 for True; if true output conditional probabilities p(s_i given backbone)")
argparser.add_argument("--unconditional_probs_only", type=int, default=0, help="0 for False, 1 for True; output unconditional probabilities p(s_i given backbone) in one forward pass")
argparser.add_argument("--backbone_noise", type=float, default=0.00, help="Standard deviation of Gaussian noise to add to backbone atoms")
argparser.add_argument("--num_seq_per_target", type=int, default=1, help="Number of sequences to generate per target")
argparser.add_argument("--batch_size", type=int, default=1, help="Batch size; can set higher for titan, quadro GPUs, reduce this if running out of GPU memory")
argparser.add_argument("--max_length", type=int, default=200000, help="Max sequence length")
argparser.add_argument("--sampling_temp", type=str, default="0.1", help="A string of temperatures, 0.2 0.25 0.5. Sampling temperature for amino acids. Suggested values 0.1, 0.15, 0.2, 0.25, 0.3. Higher values will lead to more diversity.")
argparser.add_argument("--out_folder", type=str, help="Path to a folder to output sequences, e.g. /home/out/")
argparser.add_argument("--pdb_path", type=str, default='', help="Path to a single PDB to be designed")
argparser.add_argument("--pdb_path_chains", type=str, default='', help="Define which chains need to be designed for a single PDB ")
argparser.add_argument("--jsonl_path", type=str, help="Path to a folder with parsed pdb into jsonl")
argparser.add_argument("--chain_id_jsonl",type=str, default='', help="Path to a dictionary specifying which chains need to be designed and which ones are fixed, if not specied all chains will be designed.")
argparser.add_argument("--fixed_positions_jsonl", type=str, default='', help="Path to a dictionary with fixed positions")
argparser.add_argument("--omit_AAs", type=list, default='X', help="Specify which amino acids should be omitted in the generated sequence, e.g. 'AC' would omit alanine and cystine.")
argparser.add_argument("--bias_AA_jsonl", type=str, default='', help="Path to a dictionary which specifies AA composion bias if neededi, e.g. {A: -1.1, F: 0.7} would make A less likely and F more likely.")
argparser.add_argument("--bias_by_res_jsonl", default='', help="Path to dictionary with per position bias.")
argparser.add_argument("--omit_AA_jsonl", type=str, default='', help="Path to a dictionary which specifies which amino acids need to be omited from design at specific chain indices")
argparser.add_argument("--pssm_jsonl", type=str, default='', help="Path to a dictionary with pssm")
argparser.add_argument("--pssm_multi", type=float, default=0.0, help="A value between [0.0, 1.0], 0.0 means do not use pssm, 1.0 ignore MPNN predictions")
argparser.add_argument("--pssm_threshold", type=float, default=0.0, help="A value between -inf + inf to restric per position AAs")
argparser.add_argument("--pssm_log_odds_flag", type=int, default=0, help="0 for False, 1 for True")
argparser.add_argument("--pssm_bias_flag", type=int, default=0, help="0 for False, 1 for True")
argparser.add_argument("--tied_positions_jsonl", type=str, default='', help="Path to a dictionary with tied positions")
```
-----------------------------------------------------------------------------------------------------
For example to make a conda environment to run ProteinMPNN:
* `conda create --name mlfold` - this creates conda environment called `mlfold`
* `source activate mlfold` - this activate environment
* `conda install pytorch torchvision torchaudio cudatoolkit=11.3 -c pytorch` - install pytorch following steps from https://pytorch.org/
-----------------------------------------------------------------------------------------------------
These are provided `examples/`:
* `submit_example_1.sh` - simple monomer example
* `submit_example_2.sh` - simple multi-chain example
* `submit_example_3.sh` - directly from the .pdb path
* `submit_example_3_score_only.sh` - return score only (model's uncertainty)
* `submit_example_4.sh` - fix some residue positions
* `submit_example_4_non_fixed.sh` - specify which positions to design
* `submit_example_5.sh` - tie some positions together (symmetry)
* `submit_example_6.sh` - homooligomer example
* `submit_example_7.sh` - return sequence unconditional probabilities (PSSM like)
* `submit_example_8.sh` - add amino acid bias
-----------------------------------------------------------------------------------------------------
Output example:
```
>3HTN, score=1.1705, global_score=1.2045, fixed_chains=['B'], designed_chains=['A', 'C'], model_name=v_48_020, git_hash=015ff820b9b5741ead6ba6795258f35a9c15e94b, seed=37
NMYSYKKIGNKYIVSINNHTEIVKALNAFCKEKGILSGSINGIGAIGELTLRFFNPKTKAYDDKTFREQMEISNLTGNISSMNEQVYLHLHITVGRSDYSALAGHLLSAIQNGAGEFVVEDYSERISRTYNPDLGLNIYDFER/NMYSYKKIGNKYIVSINNHTEIVKALNAFCKEKGILSGSINGIGAIGELTLRFFNPKTKAYDDKTFREQMEISNLTGNISSMNEQVYLHLHITVGRSDYSALAGHLLSAIQNGAGEFVVEDYSERISRTYNPDLGLNIYDFER
>T=0.1, sample=1, score=0.7291, global_score=0.9330, seq_recovery=0.5736
NMYSYKKIGNKYIVSINNHTEIVKALKKFCEEKNIKSGSVNGIGSIGSVTLKFYNLETKEEELKTFNANFEISNLTGFISMHDNKVFLDLHITIGDENFSALAGHLVSAVVNGTCELIVEDFNELVSTKYNEELGLWLLDFEK/NMYSYKKIGNKYIVSINNHTDIVTAIKKFCEDKKIKSGTINGIGQVKEVTLEFRNFETGEKEEKTFKKQFTISNLTGFISTKDGKVFLDLHITFGDENFSALAGHLISAIVDGKCELIIEDYNEEINVKYNEELGLYLLDFNK
>T=0.1, sample=2, score=0.7414, global_score=0.9355, seq_recovery=0.6075
NMYKYKKIGNKYIVSINNHTEIVKAIKEFCKEKNIKSGTINGIGQVGKVTLRFYNPETKEYTEKTFNDNFEISNLTGFISTYKNEVFLHLHITFGKSDFSALAGHLLSAIVNGICELIVEDFKENLSMKYDEKTGLYLLDFEK/NMYKYKKIGNKYVVSINNHTEIVEALKAFCEDKKIKSGTVNGIGQVSKVTLKFFNIETKESKEKTFNKNFEISNLTGFISEINGEVFLHLHITIGDENFSALAGHLLSAVVNGEAILIVEDYKEKVNRKYNEELGLNLLDFNL
```
* `score` - average over residues that were designed negative log probability of sampled amino acids
* `global score` - average over all residues in all chains negative log probability of sampled/fixed amino acids
* `fixed_chains` - chains that were not designed (fixed)
* `designed_chains` - chains that were redesigned
* `model_name/CA_model_name` - model name that was used to generate results, e.g. `v_48_020`
* `git_hash` - github version that was used to generate outputs
* `seed` - random seed
* `T=0.1` - temperature equal to 0.1 was used to sample sequences
* `sample` - sequence sample number 1, 2, 3...etc
-----------------------------------------------------------------------------------------------------
```
@article{dauparas2022robust,
title={Robust deep learning--based protein sequence design using ProteinMPNN},
author={Dauparas, Justas and Anishchenko, Ivan and Bennett, Nathaniel and Bai, Hua and Ragotte, Robert J and Milles, Lukas F and Wicky, Basile IM and Courbet, Alexis and de Haas, Rob J and Bethel, Neville and others},
journal={Science},
volume={378},
number={6615},
pages={49--56},
year={2022},
publisher={American Association for the Advancement of Science}
}
```
-----------------------------------------------------------------------------------------------------
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1 change: 1 addition & 0 deletions ProteinMPNN/colab_notebooks/README.md
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<a href="https://colab.research.google.com/github/dauparas/ProteinMPNN/blob/main/colab_notebooks/quickdemo.ipynb" target="_parent"><img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/></a>
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