SimpleDH3

Code for "Simple End-to-end Deep Learning Model for CDR-H3 Loop Structure Prediction" paper accepted at Machine Learning for Structural Biology (MLSB) Workshop at NeurIPS 2021

NB! This repo is in the process, we will update instructions and the code in the beginning of 2022

Setup development environment

• Install requirements from requirements.txt

Data

The data can be created using script data/create_data.py by providing summary file from SAbDab. Two files will be produced: with sequnces and with coordinates.

Usage

Firstly, embeddings needs to be created:

cd modules
python3 embedding/data_to_embedding.py

To train model, run:

bash train.sh

To evaluate model, run:

bash predict_test.sh