Table 4.

List of deep learning‐based MHC‐peptide binding prediction tools

No.	Software	MHC Type	Core network model	Framework	Group	Data Typea)	Input encoding	Usability b)	Year	Reference
1	ConvMHC	MHC Class I	CNN	Keras	Pan‐specific	BA	Handcrafted features	W,P	2017	[142]
2	HLA‐CNN	MHC Class I	CNN	keras/Theano	Allele‐specific	BA	Word embedding	O,C,T	2017	[143]
3	DeepMHC	MHC Class I	CNN	‐	Allele‐specific	BA	One‐hot	‐	2017	[144]
4	DeepSeqPan	MHC Class I	CNN	Keras/Tensorflow	Pan‐specific	BA	One‐hot	O,C,P,T	2019	[145]
5	AI‐MHC	MHC Class I/II	CNN	TensorFlow	Pan‐specific	BA	Word embedding	W,P	2018	[155]
6	DeepSeqPanII	MHC Class II	CNN+RNN	PyTorch	Pan‐specific	BA	One‐hot + BLOSUM	O,C,P,T	2019	[154]
7	MHCSeqNet	MHC Class I	RNN	Keras/Tensorflow	Pan‐specific	BA	Word embedding	O,C,P,T	2019	[146]
8	MARIA	MHC Class II	RNN	Keras/Tensorflow	Pan‐specific	BA + MS	One‐hot	W,P	2019	[138]
9	MHCflurry	MHC Class I	CNN	Keras/Tensorflow	Allele‐specific	BA + MS	BLOSUM	O,C,P,T	2018	[147]
10	DeepHLApan	MHC Class I	RNN	Keras/Tensorflow	Pan‐specific	BA + MS	Word embedding	O,C,W,P	2019	[148]
11	ACME	MHC Class I	CNN	Keras/Tensorflow	Pan‐specific	BA	BLOSUM	O,C,P,T	2019	[149]
12	EDGE	MHC Class I	DNN	Keras/Theano	Allele‐specific	MS	One‐hot	O	2019	[137]
13	CNN‐NF	MHC Class I	CNN	MXNet	Allele‐specific	BA + MS	Handcrafted features	O	2019	[150]
14	MHCnuggets	MHC Class I/II	RNN	Keras/Tensorflow	Allele‐specific	BA + MS	One‐hot	O,C,P,T	2019	[156]
15	DeepNeo	MHC Class I	CNN	Theano	Pan‐specific	BA	2D interaction map	‐	2020	[151]
16	DeepLigand	MHC Class I	CNN	PyTorch	Pan‐specific	BA + MS	Word embedding + BLOSUM + One‐hot	O,C,P,T	2019	[152]
17	PUFFIN	MHC Class I/II	CNN	PyTorch	Pan‐specific	BA	One‐hot + BLOSUM	O,C,P,T	2019	[157]
18	NeonMHC2	MHC Class II	CNN	Keras/Tensorflow	Allele‐specific	MS	Handcrafted features	O,C,W,P,T	2019	[139]
19	USMPep	MHC Class I/II	RNN	PyTorch	Allele‐specific	BA	Word embedding	O,T	2020	[158]
20	MHCherryPan	MHC Class I	CNN+RNN	Keras/Tensorflow	Pan‐specific	BA	BLOSUM	‐	2019	[153]
21	DeepAttentionPan	MHC Class I	CNN	PyTorch	Pan‐specific	BA	BLOSUM	O,C,P,T	2019	[141]

^a)BA, binding assay data; MS, eluted ligand data from mass spectrometry experiments;

^b)O, open‐source; C, command line; P, provide trained model for prediction; W, web interface; T, provide option for model training. The link of each tool could be found at https://github.com/bzhanglab/deep_learning_in_proteomics.