/energy_model4antibody_design

Energy-based Model for Antibody Design

Primary LanguagePython

antibody CDR loop design

This repository hosts an open-source code for the paper entitled Antibody Complementarity Determining Regions (CDRs) design using Constrained Energy Model (KDD 2022). The paper is available at https://dl.acm.org/doi/abs/10.1145/3534678.3539285

environment

setup

conda create -n antibody python=3.7
conda activate antibody 
pip install torch 
pip install tqdm 
pip install bio

activate

conda activate antibody

data

CoV-AbDab: the CoronaVirus Antibody Database

the Coronavirus Antibody Database (CoV-AbDab) is a database containing the oV-AbDab contains data on over published and patented antibodies and nanobodies known to bind to at least one betacoronavirus. It is available at http://opig.stats.ox.ac.uk/webapps/covabdab/.

SAbDab: the Structural Antibody Database

SAbDab collects, curates and presents antibody structures from the PDB in an consistent manner. It is available at http://opig.stats.ox.ac.uk/webapps/newsabdab/sabdab/

wget http://opig.stats.ox.ac.uk/webapps/newsabdab/sabdab/archive/all/

It takes around 4G.

python data.py

output: data/sabdab/H1.txt, data/sabdab/H2.txt, data/sabdab/H3.txt

python data_analysis.py

model: constrained energy model

python train.py