prescient-igloo 0.1.0

Tokenizing Loops of Antibodies (arXiv:2509.08707)

Igloo: Tokenizing Loops of Antibodies

Preprint

Authors

• Ada Fang
• Rob Alberstein
• Simon Kelow
• Frédéric Dreyer

:seedling: Getting started

Clone the repo: git clone https://github.com/prescient-design/ibex.git

Create an environment and install igloo locally

uv venv --python 3.11
source .venv/bin/activate
uv pip install -e .

Alternatively, you can install the prescient-igloo package

pip install prescient-igloo

which provides the model/ directory as import igloo and the finetune_igbert/ directory as import igloo.plm.

:rocket: Run Igloo

For loops with sequences and structures ( :star2: recommended)

If structures are available use this approach

1. Prepare input to Igloo Prepare a CSV file, see example/sample_igloo_sequences.csv containing sequences of heavy and light chains. Required columns:

• fv_heavy_aho and fv_light_aho sequences of aho aligned heavy and light chains. For aho alignments of sequences please refer to ANARCI.
• id unique identifier for each antibody that should correspond to the file name <id>.pdb in the structure_dir.

python process_data/process_dihedrals.py \
    --id_key "id" --aho_light_key "fv_light_aho" --aho_heavy_key "fv_heavy_aho" \
    --structure_dir my_pdbs/ \
    --df_path example/sample_igloo_sequences.csv \
    --parquet_output_path example/sample_igloo_input.parquet

The output file will have loops with loop_id, where it is the sequence id with _{loop_type} as a suffix and loop_type is one of [H1, H2, H3, H3, L1, L2, L3, L4].

Alternatively, you can write your own processing script to output something like the example example/sample_igloo_input.parquet.

2. Igloo Inference

/homefs/home/fanga5/micromamba/envs/pyenv/bin/python run_igloo.py \
    --model_ckpt checkpoints/igloo_weights.pt \
    --model_config checkpoints/igloo_config.json \
    --loop_dataset_path example/sample_igloo_input.parquet \
    --output_path example/sample_igloo_output.parquet

For loops with sequences and predicted structures ( :star: recommended)

Igloo can be used for library design by:

• Finding sequences close to the seed which are in the same Igloo cluster to the seed
• Downsampling a large library by maximizing coverage over the Igloo clusters

1. Prepare your sequences

CSV file, see example/sample_igloo_sequences.csv, containing sequences of heavy and light chains. Required columns:

• fv_heavy and fv_light sequences of heavy and light chains.
• fv_heavy_aho and fv_light_aho sequences of aho aligned heavy and light chains. For aho alignments of sequences please refer to ANARCI.
• id unique identifier for each antibody chain sequence, can be just a unique number for each sequence.

2. Run structure prediction

Igloo can tokenize loops with sequence only, but performs better if it has structures of the antibodies. Generate structures with a structure predictor, e.g. Ibex which is provided in the Prescient repo.

pip install prescient-ibex
ibex --csv example/sample_igloo_sequences.csv --output ibex_predictions_dir/

3. Prepare input to Igloo

python process_data/process_dihedrals.py \
    --id_key "id" --aho_light_key "fv_light_aho" --aho_heavy_key "fv_heavy_aho" \
    --structure_dir ibex_predictions_dir/ \
    --df_path example/sample_igloo_sequences.csv \
    --parquet_output_path example/sample_igloo_input.parquet

The output file will have loops with loop_id, where it is the sequence id with _{loop_type} as a suffix and loop_type is one of [H1, H2, H3, H3, L1, L2, L3, L4].

4. Igloo Inference

python run_igloo.py \
    --model_ckpt checkpoints/igloo_weights.pt \
    --model_config checkpoints/igloo_config.json \
    --loop_dataset_path example/sample_igloo_input.parquet \
    --output_path example/sample_igloo_output.parquet

For loops with only sequences and without predicted structures

This may be preferable if there are many sequences (i.e. millions) and running structure prediction on all of the sequences is too compute intensive.

To run Igloo with sequence only, prepare a CSV file with the columns:

• loop_id: Unique identifier for each loop
• loop_sequence: One letter amino acid sequence for loop

An example is provided at example/sample_igloo_input_sequence_only.csv.

python run_igloo.py \
    --model_ckpt checkpoints/igloo_weights.pt \
    --model_config checkpoints/igloo_config.json \
    --loop_dataset_path example/sample_igloo_input_sequence_only.csv \
    --output_path example/sample_igloo_out_sequence_only.parquet

Igloo output

The output is a parquet file with the following columns:

• loop_id
• encoded: Continuous Igloo representation
• quantized: Discrete Igloo representation, this is the encoded representation after it is passed through the Vector Quantize layer
• quantized_indices: An integer indicating which discrete Igloo token

:snowflake: Training Igloo

Igloo was first trained on SAbDab and Ibex-predicted pOAS structures. Then finetuned on just SAbDab.

python train.py \
    --train_data_path poas_sabdab_train.jsonl \
    --val_data_path sabdab_val.jsonl \
    --batch_size 64 \
    --learning_rate 1e-3 \
    --project_name "Phase 1: train on sabdab+pOAS" \
    --device cuda \
    --num_epochs 100 \
    --codebook_size 8192 \
    --num_encoder_layers 4 \
    --commit_loss_weight 0.5 \
    --save_dir Igloo_models \
    --embedding_dim 128 \
    --unit_circle_transform_weight 0.01 \
    --loop_length_tolerance 0 \
    --dihedral_loss \
    --learnable_codebook \
    --use_wandb

python train.py \
    --train_data_path sabdab_train.jsonl \
    --val_data_path sabdab_val.jsonl \
    --batch_size 64 \
    --learning_rate 5e-5 \
    --project_name "Phase 2: finetune on sabdab only" \
    --device cuda \
    --num_epochs 100 \
    --codebook_size 8192 \
    --num_encoder_layers 4 \
    --commit_loss_weight 0.5 \
    --save_dir Igloo_models \
    --embedding_dim 128 \
    --unit_circle_transform_weight 0.01 \
    --loop_length_tolerance 0 \
    --dihedral_loss \
    --learnable_codebook \
    --codebook_learning_rate 1e-3 \
    --weight_decay 1e-5 \
    --pretrained_model_weights Igloo_models/best_checkpoint_from_above.pt \
    --pretrained_model_config Igloo_models/model_config_from_above.json \
    --use_wandb

:robot: IglooLM and IglooALM

Please refer to finetune_igbert/README.md.

:bulb: Tutorials and reproducing paper analyses

Recovery of canonical clusters

See: paper_analyses/1_recovery_of_canonical_clusters/recovery_of_canonical_clusters.ipynb

We show how well Igloo can recovery the canonical clusters (North et al. 2011, Kelow et al. 2022) across SAbDab with dihedral distance cutoffs of 0.1 and 0.47. The results can be seen at the bottom of the jupyter notebook.

Retrieval of similar structured loops with Igloo tokens

See: paper_analyses/2_retrieve_similar_loops/sabdab_test_set.ipynb

We show how to use Igloo embeddings to retrieve similar structured loops. Baselines can be run at paper_analyses/0_baselines.

Predicting binding affinity with IglooLM embeddings on AbBiBench

See: paper_analyses/3_abbibench/run_abbibench.py. Baselines can be run at paper_analyses/0_baselines.

Sampling structurally-consistent loop sequences with IglooALM

See: paper_analyses/4_sampled_cdrs/analyse_sampled_cdrs.ipynb.

Citation

@misc{fang2025tokenizingloopsantibodies,
      title={Tokenizing Loops of Antibodies}, 
      author={Ada Fang and Robert G. Alberstein and Simon Kelow and Frédéric A. Dreyer},
      year={2025},
      eprint={2509.08707},
      archivePrefix={arXiv},
      primaryClass={q-bio.BM},
      url={https://arxiv.org/abs/2509.08707}, 
}

:hammer_and_wrench: Support

Please feel free to contact Ada Fang ([e-mail]) of Frédéric Dreyer ([e-mail]) for any questions or help with running Igloo.