Neoantigen-targeted TCR-engineered T cell immunotherapy: current advances and challenges

Biomarker Research

Table 2 Currently available TCR-epitope binding prediction methods

TCR-epitope binding prediction tool	Predictable TCR chain(s)	Epitope constraint	TCR length constraint	Method description	Published date	Software / Webserver
TCRex	TCR β	Restricted epitopes	None	Models based on random forest classifiers	Nov-2019	Webserver:
TCRex	TCR β	Restricted epitopes	None	Models based on random forest classifiers	Nov-2019	https://www.tcrex.biodatamining.be/
ERGO-LSTM	TCR β	None	None	LSTM based model	Aug-2020	Software:
ERGO-LSTM	TCR β	None	None	LSTM based model	Aug-2020	https://github.com/louzounlab/ERGO
ERGO-AE	TCR β	None	None	Autoencoder based model	Aug-2020	Software:
ERGO-AE	TCR β	None	None	Autoencoder based model	Aug-2020	https://github.com/louzounlab/ERGO
ImRex	TCR β	8 ~ 11-mer	10 ~ 20	Dual input CNN model	Dec-2020	Software:
ImRex	TCR β	8 ~ 11-mer	10 ~ 20	Dual input CNN model	Dec-2020	https://github.com/pmoris/ImRex
DLpTCR	TCR αβ	9-mer	8 ~ 20	Ensemble deep learning model of FCN, LeNet-5 and ResNet	Jul-2021	Software:
						https://github.com/jiangBiolab/DLpTCR
						Webserver:
						http://jianglab.org.cn/DLpTCR/
NetTCR-2.0	TCR αβ	9-mer	8 ~ 18	1-dimensional CNN model	Sep-2021	Software:
						https://github.com/mnielLab/NetTCR-2.0/
						Webserver:
						https://services.healthtech.dtu.dk/service.php?NetTCR-2.0
pMTnet	TCR β	None	None	deep neural network based on LSTM and stacked autoencoders	Sep-2021	Software:
pMTnet	TCR β	None	None	deep neural network based on LSTM and stacked autoencoders	Sep-2021	https://github.com/tianshilu/pMTnet

Abbreviations LSTM Long short-term memory, CNN,Convolutional neural network, FCN Fully convolutional networks, ResNet Residual neural network

ISSN: 2050-7771