MultiSAAl: Sequence-informed Antibody-Antigen Interactions Prediction using Multi-scale Deep Learning

🧪 Method Overview

Input the antibody heavy chain variable region, light chain variable region and antigen sequence to predict the binding probability of antibody and antigen.

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🚀 Getting Started

To run this project, You should make sure you have ANARCI and CALIBER installed. In addition: numpy==1.22.4 pandas==1.4.3 scikit_learn==1.2.2 scipy==1.7.3 torch==1.12.1 tqdm==4.64.1 transformers==4.24.0

🏃 Running the MultiSAAI

After installation, run CALIBER to extract epitopes and CDR-H3 to generate functional features: feature/abag

Functional Features: feature/abag
Manual Features:feature/miler

Insert features into: trainer/bert_finetuning_er_trainer_sabdab.py (bert_finetuning_er_trainer_covabdab.py) 💡 Example: Run MultiSAAI run_train.sh/Online Server (http://zhanglab-bioinf.com/MultiSAAI/)