This repo contains the code for our paper " Drug-target binding affinity prediction using message passing neural network and self supervised method"
by Leiming Xia, Zhen Li*
We report UCMCDTA, an deep learning model for binding affinity prediction tasks. This model using an undirected-CMPNN for molecule embedding and MCPCProt models for protein embedding. Both embeddings are concatenated for DTA prediction. The results showed that the proposed model outperformed other deep learning methods, which also provides a novel strategy for deep learning-based virtual screening methods.
- Python 3.7
- Pytorch
- numpy
- pickle
- RDKit
- sklearn
- CUDA
to test BindingDB Ki dataset: first
cd ki
and then run
python dataProcess.py
to generate the files required. Then
cd ..
python main.py --dataset ki --mode regression
We'd like to express our gratitude towards all the colleagues and reviewers for helping us improve the paper.