DeepGS

Source Code Repository for DeepGS: Deep Representation Learning of Graphs and Sequences for Drug-Target Binding Affinity Prediction. Please refer to our paper for detailed (ECAI 2020 will be held soon )

Installation

We recommend to create a new environment.

conda create -n deepgs python=3.7.6
source activate deepgs

DeepGS is implemented based on Pytorch, RDKit and pytorch-geometric.

git clone https://github.com/jacklin18/DeepGS.git  
cd DeepGS  
pip install -r requirements.txt

Data

Please see the DeepDTA for detailed information. In order to train the DeepGS model, you must provide training data with each row contains a molecule (i.e., SMILES strings), a protein sequence (i.e., amino acids) and a label between the drug-target pair (i.e., binding affinity value). For example:

CC1=C2C=C(C=CC2=NN1)C3=CC(=CN=C3)OCC(CC4=CC=CC=C4)N MKKFFDSRREQGGSGLGSGSSGGGGSTSGLGSGYIGRVFGIGRQQVTVDEVLAEGGFAIVFLVRTSNGMKCALKRMFVNNEHDLQVCKREIQIMRDLSGHKNIVGYIDSSINNVSSGDVWEVLILMDFCRGGQVVNLMNQRLQTGFTENEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLHDRGHYVLCDFGSATNKFQNPQTEGVNAVEDEIKKYTTLSYRAPEMVNLYSGKIITTKADIWALGCLLYKLCYFTLPFGESQVAICDGNFTIPDNSRYSQDMHCLIRYMLEPDPDKRPDIYQVSYFSFKLLKKECPIPNVQNSPIPAKLPEPVKASEAAAKKTQPKARLTDPIPTTETSIAPRQRPKAGQTQPNPGILPIQPALTPRKRATVQPPPQAAGSSNQPGLLASVPQPKPQAPPSQPLPQTQAKQPQAPPTPQQTPSTQAQGLPAQAQATPQHQQQLFLKQQQQQQQPPPAQQQPAGTFYQQQQAQTQQFQAVHPATQKPAIAQFPVVSQGGSQQQLMQNFYQQQQQQQQQQQQQQLATALHQQQLMTQQAALQQKPTMAAGQQPQPQPAAAPQPAPAQEPAIQAPVRQQPKVQTTPPPAVQGQKVGSLTPPSSPKTQRAGHRRILSDVTHSAVFGVPASKSTQLLQAAAAEASLNKSKSATTTPSGSPRTSQQNVYNPSEGSTWNPFDDDNFSKLTAEELLNKDFAKLGEGKHPEKLGGSAESLIPGFQSTQGDAFATTSFSAGTAEKRKGGQTVDSGLPLLSVSDPFIPLQVPDAPEKLIEGLKSPDTSLLLPDLLPMTDPFGSTSDAVIEKADVAVESLIPGLEPPVPQRLPSQTESVTSNRTDSLTGEDSLLDCSLLSNPTTDLLEEFAPTAISAPVHKAAEDSNLISGFDVPEGSDKVAEDEFDPIPVLITKNPQGGHSRNSSGSSESSLPNLARSLLLVDQLIDL 43.0
...

Usage

(i) preprocess data as input

cd code
sh/bash preprocess.sh

(ii) train the model

sh/bash run_tranining.sh

Citation

If you use the code of DeepGS, please cite the paper below:

@inproceedings{lin2020deepgs,
title ={DeepGS: Deep Representation Learning of Graphs and Sequences for Drug-Target Binding Affinity Prediction},
author ={Lin, Xuan and Zhao, Kaiqi and Xiao, Tong and Quan, Zhe and Wang, Zhi-Jie and Yu, Philip S},
booktitle ={24th European Conference on Artificial Intelligence (ECAI)},
pages ={1--8},
year ={2020}
}