antifold 0.3.1
Inverse folding of antibodies

AntiFold
==============================

AntiFold predicts sequences which fit into antibody variable domain structures. The tool outputs residue log-likelihoods in [CSV format](https://github.com/oxpig/AntiFold/blob/master/output/single_pdb/6y1l_imgt.csv), and can sample sequences to a [FASTA format](https://github.com/oxpig/AntiFold/blob/master/output/single_pdb/6y1l_imgt.fasta) directly. Sampled sequences show high structural agreement with experimental structures.

AntiFold is based on the ESM-IF1 model and is fine-tuned on solved and predicted antibody structures from SAbDab and OAS.

- Paper: [arXiv pre-print](https://arxiv.org/abs/2405.03370)
- Webserver: [OPIG webserver](https://opig.stats.ox.ac.uk/webapps/antifold/)
- Colab: [![Open In Colab](images/colab-badge.svg)](https://colab.research.google.com/drive/1oEDJCHcwxGBeCiYsCm62_OHBXDHnlhb9)
- Model: [model.pt](https://opig.stats.ox.ac.uk/data/downloads/AntiFold/models/model.pt)
- License: [BSD 3-Clause](https://opig.stats.ox.ac.uk/data/downloads/AntiFold/LICENSE)

## Webserver

To try AntiFold without installing it, please see our OPIG webserver:
[https://opig.stats.ox.ac.uk/webapps/antifold/](https://opig.stats.ox.ac.uk/webapps/antifold/)

## Install and run AntiFold

#### Download and install from Github source (recommended - latest release)
```bash
conda create --name antifold python=3.10 -y && conda activate antifold
conda install -c conda-forge pytorch
git clone https://github.com/oxpig/AntiFold && cd AntiFold
pip install .
```

GPU only: install using environment.yml

```bash
conda create env -f environment.yml
python -m pip install .
```

Depending on your CUDA version you may need to change the dependency `pytorch-cuda=12.1` in the environment.yml file.
Detailed instructions on how to correctly install pytorch for your system can be found [here](https://pytorch.org/get-started/locally/)

#### Run AntiFold (inverse-folding probabilities, sample sequences)
```bash
# Run AntiFold on single PDB/CIF file
# Nb: Assumes first chain heavy, second chain light
python antifold/main.py \
    --pdb_file data/pdbs/6y1l_imgt.pdb

# Antibody-antigen complex
python antifold/main.py \
    --pdb_file data/antibody_antigen/3hfm.pdb \
    --heavy_chain H \
    --light_chain L \
    --antigen_chain Y

# Nanobody or single-chain
python antifold/main.py \
    --pdb_file data/nanobody/8oi2_imgt.pdb \
    --nanobody_chain B

# Folder of PDB/CIFs
# Nb: Assumes first chain heavy, second light
python antifold/main.py \
    --pdb_dir data/pdbs

# Specify chains to run in a CSV file (e.g. antibody-antigen complex)
python antifold/main.py \
    --pdb_dir data/antibody_antigen \
    --pdbs_csv data/antibody_antigen.csv

# Sample sequences 10x
python antifold/main.py \
    --pdb_file data/pdbs/6y1l_imgt.pdb \
    --heavy_chain H \
    --light_chain L \
    --num_seq_per_target 10 \
    --sampling_temp "0.2" \
    --regions "CDR1 CDR2 CDR3"

# Run all chains with ESM-IF1 model weights
python antifold/main.py \
    --pdb_dir data/pdbs \
    --esm_if1_mode
```

## Jupyter notebook
Notebook: <a href="https://github.com/oxpig/AntiFold/blob/master/notebook.ipynb">notebook.ipynb</a>

Colab: [![Open In Colab](images/colab-badge.svg)](https://colab.research.google.com/drive/1oEDJCHcwxGBeCiYsCm62_OHBXDHnlhb9)

```python
import antifold
import antifold.main

# Load model
model = antifold.main.load_model()

# PDB directory
pdb_dir = "data/pdbs"

# Assumes first chain heavy, second chain light
pdbs_csv = antifold.main.generate_pdbs_csv(pdb_dir, max_chains=2)

# Sample from PDBs
df_logits_list = antifold.main.get_pdbs_logits(
    model=model,
    pdbs_csv_or_dataframe=pdbs_csv,
    pdb_dir=pdb_dir,
)

# Output log probabilites
df_logits_list[0]
```

## Input parameters
Required parameters:
```text
Input PDBs should be antibody variable domain structures (IMGT positions 1-128).

If no chains are specified, the first two chains will be assumed to be heavy light.
If custom_chain_mode is set, all (10) chains will be run.

- Option 1: PDB file (--pdb_file). We recommend specifying heavy and light chain (--heavy_chain and --light_chain)
- Option 2: PDB folder (--pdb_dir) + CSV file specifying chains (--pdbs_csv)
- Option 3: PDB folder, infer 1st chain heavy, 2nd chain light
```

Parameters for generating new sequences:
```text
PDBs should be IMGT annotated for the sequence sampling regions to be valid.

- Number of sequences to generate (--num_seq_per_target)
- Region to mutate (--region) based on inverse folding probabilities. Select from list in IMGT_dict (e.g. 'CDRH1 CDRH2 CDRH3')
- Sampling temperature (--sampling_temp) controls generated sequence diversity, by scaling the inverse folding probabilities before sampling. Temperature = 1 means no change, while temperature ~ 0 only samples the most likely amino-acid at each position (acts as argmax).
```

Optional parameters:
```text
- Multi-chain mode for including antigen or other chains (--custom_chain_mode)
- Extract latent representations of PDB within model (--extract_embeddings)
- Use ESM-IF1 instead of AntiFold model weights (--esm_if1_mode), enables custom_chain_mode
```

## Example output
For example webserver output, see:
[https://opig.stats.ox.ac.uk/webapps/antifold/results/example_job/](https://opig.stats.ox.ac.uk/webapps/antifold/results/example_job/)

Output CSV with residue log-probabilities: Residue probabilities: <a href="https://github.com/oxpig/AntiFold/blob/master/output/example_pdbs/6y1l_imgt.csv">6y1l_imgt.csv</a>
- pdb_pos - PDB residue number
- pdb_chain - PDB chain
- aa_orig - PDB residue (e.g. 112)
- aa_pred - Top predicted residue by AntiFold (i.e. argmax) for this position
- pdb_posins - PDB residue number with insertion code (e.g. 112A)
- perplexity - Inverse folding tolerance (higher is more tolerant) to mutations. See paper for more details.
- Amino-acids - Inverse folding scores (log-likelihood) for the given position
```csv
pdb_pos,pdb_chain,aa_orig,aa_pred,pdb_posins,perplexity,A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y
2,H,V,M,2,1.6488,-4.9963,-6.6117,-6.3181,-6.3243,-6.7570,-4.2518,-6.7514,-5.2540,-6.8067,-5.8619,-0.0904,-6.5493,-4.8639,-6.6316,-6.3084,-5.1900,-5.0988,-3.7295,-8.0480,-7.3236
3,H,Q,Q,3,1.3889,-10.5258,-12.8463,-8.4800,-4.7630,-12.9094,-11.0924,-5.6136,-10.9870,-3.1119,-8.1113,-9.4382,-6.2246,-13.3660,-0.0701,-4.9957,-10.0301,-6.8618,-7.5810,-13.6721,-11.4157
4,H,L,L,4,1.0021,-13.3581,-12.6206,-17.5484,-12.4801,-9.8792,-13.6382,-14.8609,-13.9344,-16.4080,-0.0002,-9.2727,-16.6532,-14.0476,-12.5943,-15.4559,-16.9103,-17.0809,-10.5670,-13.5334,-13.4324
...
```

Output FASTA file with sampled sequences: <a href="https://github.com/oxpig/AntiFold/blob/master/output/example_pdbs/6y1l_imgt.fasta">6y1l_imgt.fasta</a>
- T: Temperature used for design
- score: average log-odds of residues in the sampled region
- global_score: average log-odds of all residues (IMGT positions 1-128)
- regions: regions selected for design
- seq_recovery: # mutations / total sequence length
- mutations: # mutations from original PDB sequence
```fasta
>6y1l_imgt , score=0.2934, global_score=0.2934, regions=['CDR1', 'CDR2', 'CDRH3'], model_name=AntiFold, seed=42
VQLQESGPGLVKPSETLSLTCAVSGYSISSGYYWGWIRQPPGKGLEWIGSIYHSGSTYYN
PSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCAGLTQSSHNDANWGQGTLVTVSS/V
LTQPPSVSAAPGQKVTISCSGSSSNIGNNYVSWYQQLPGTAPKRLIYDNNKRPSGIPDRF
SGSKSGTSATLGITGLQTGDEADYYCGTWDSSLNPVFGGGTKLEIKR
> T=0.20, sample=1, score=0.3930, global_score=0.1869, seq_recovery=0.8983, mutations=12
VQLQESGPGLVKPSETLSLTCAVSGASITSSYYWGWIRQPPGKGLEWIGSIYYSGSTYYN
PSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCAGLYGSPWSNPYWGQGTLVTVSS/V
LTQPPSVSAAPGQKVTISCSGSSSNIGNNYVSWYQQLPGTAPKRLIYDNNKRPSGIPDRF
SGSKSGTSATLGITGLQTGDEADYYCGTWDSSLNPVFGGGTKLEIKR
...
```

## Usage
```bash
usage:
    # Predict on example PDBs in folder
python antifold/main.py \
    --pdb_file data/antibody_antigen/3hfm.pdb \
    --heavy_chain H \
    --light_chain L \
    --antigen_chain Y # Optional

Predict inverse folding probabilities for antibody variable domain, and sample sequences with maintained fold.
PDB structures should be IMGT-numbered, paired heavy and light chain variable domains (positions 1-128).

For IMGT numbering PDBs use SAbDab or https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabpred/anarci/

options:
  -h, --help            show this help message and exit
  --pdb_file PDB_FILE   Input PDB file (for single PDB predictions)
  --heavy_chain HEAVY_CHAIN
                        Ab heavy chain (for single PDB predictions)
  --light_chain LIGHT_CHAIN
                        Ab light chain (for single PDB predictions)
  --antigen_chain ANTIGEN_CHAIN
                        Antigen chain (optional)
  --pdbs_csv PDBS_CSV   Input CSV file with PDB names and H/L chains (multi-PDB predictions)
  --pdb_dir PDB_DIR     Directory with input PDB files (multi-PDB predictions)
  --out_dir OUT_DIR     Output directory
  --regions REGIONS     Space-separated regions to mutate. Default 'CDR1 CDR2 CDR3H'
  --num_seq_per_target NUM_SEQ_PER_TARGET
                        Number of sequences to sample from each antibody PDB (default 0)
  --sampling_temp SAMPLING_TEMP
                        A string of temperatures e.g. '0.20 0.25 0.50' (default 0.20). Sampling temperature for amino acids. Suggested values 0.10, 0.15, 0.20, 0.25, 0.30. Higher values will lead to more diversity.
  --limit_variation     Limit variation to as many mutations as expected from temperature sampling
  --extract_embeddings  Extract per-residue embeddings from AntiFold / ESM-IF1
  --custom_chain_mode   Run all specified chains (for antibody-antigen complexes or any combination of chains)
  --exclude_heavy       Exclude heavy chain from sampling
  --exclude_light       Exclude light chain from sampling
  --batch_size BATCH_SIZE
                        Batch-size to use
  --num_threads NUM_THREADS
                        Number of CPU threads to use for parallel processing (0 = all available)
  --seed SEED           Seed for reproducibility
  --model_path MODEL_PATH
                        Alternative model weights (default models/model.pt). See --use_esm_if1_weights flag to use ESM-IF1 weights instead of AntiFold
  --esm_if1_mode        Use ESM-IF1 weights instead of AntiFold
  --verbose VERBOSE     Verbose printing
```

## IMGT regions dict
Used to specify which regions to mutate in an IMGT numbered PDB
- IMGT numbered PDBs: [https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab](https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab)
- Renumber existing PDBs with ANARCI: [https://github.com/oxpig/ANARCI](https://github.com/oxpig/ANARCI)
- Read more: [https://www.imgt.org/IMGTScientificChart/Numbering/IMGTIGVLsuperfamily.html](https://www.imgt.org/IMGTScientificChart/Numbering/IMGTIGVLsuperfamily.html)

```python
IMGT_dict = {
    "all": range(1, 128 + 1),
    "allH": range(1, 128 + 1),
    "allL": range(1, 128 + 1),
    "FWH": list(range(1, 26 + 1)) + list(range(40, 55 + 1)) + list(range(66, 104 + 1)),
    "FWL": list(range(1, 26 + 1)) + list(range(40, 55 + 1)) + list(range(66, 104 + 1)),
    "CDRH": list(range(27, 39)) + list(range(56, 65 + 1)) + list(range(105, 117 + 1)),
    "CDRL": list(range(27, 39)) + list(range(56, 65 + 1)) + list(range(105, 117 + 1)),
    "FW1": range(1, 26 + 1),
    "FWH1": range(1, 26 + 1),
    "FWL1": range(1, 26 + 1),
    "CDR1": range(27, 39),
    "CDRH1": range(27, 39),
    "CDRL1": range(27, 39),
    "FW2": range(40, 55 + 1),
    "FWH2": range(40, 55 + 1),
    "FWL2": range(40, 55 + 1),
    "CDR2": range(56, 65 + 1),
    "CDRH2": range(56, 65 + 1),
    "CDRL2": range(56, 65 + 1),
    "FW3": range(66, 104 + 1),
    "FWH3": range(66, 104 + 1),
    "FWL3": range(66, 104 + 1),
    "CDR3": range(105, 117 + 1),
    "CDRH3": range(105, 117 + 1),
    "CDRL3": range(105, 117 + 1),
    "FW4": range(118, 128 + 1),
    "FWH4": range(118, 128 + 1),
    "FWL4": range(118, 128 + 1),
}
```

## Citing this work

The code and data in this package is based on the following paper <a href="https://arxiv.org/abs/2405.03370">AntiFold</a>. If you use it, please cite:

```tex
@misc{antifold,
      title={AntiFold: Improved antibody structure-based design using inverse folding},
      author={Magnus Haraldson Høie and Alissa Hummer and Tobias H. Olsen and Broncio Aguilar-Sanjuan and Morten Nielsen and Charlotte M. Deane},
      year={2024},
      eprint={2405.03370},
      archivePrefix={arXiv},
      primaryClass={q-bio.BM}
}
```