Table 1.

Summary of some of the most recent or most widely used human leukocyte antigen (HLA)-I predictors with available web interface or code repository.

Name	Training data	Output	Algorithm	Allele coverage	Access	Reference
NetMHC4.0	BA	BA	NN	S	http://www.cbs.dtu.dk/services/NetMHC/	(110)
NetMHCpan4.0	BA + MS	R (BA)	NN	Pan	http://www.cbs.dtu.dk/services/NetMHCpan-4.0/	(117)
MixMHCpred	MS	R	PWM	S	https://github.com/GfellerLab/MixMHCpred	(72, 120)
MHCflurry	BA	BA	NN	S	https://github.com/openvax/mhcflurry	(113)
PickPocket	BA	BA	PWM	Pan	http://www.cbs.dtu.dk/services/PickPocket/	(107)
NetMHCstabpan	BS	BS	NN	Pan	http://www.cbs.dtu.dk/services/NetMHCstabpan/	(118)
NetMHCstab	BS	BS	NN	S	http://www.cbs.dtu.dk/services/NetMHCstab/	(111)
NetMHCcons	BA	BA	C	S	http://www.cbs.dtu.dk/services/NetMHCcons/	(181)
IEDB consensus	BA	R	C	S	http://tools.iedb.org/mhci/	(182)
SMMPMBEC	BA	R	PWM	S	https://github.com/ykimbiology/smmpmbec	(104)
MHCnuggets	BA	BA	NN	S	https://github.com/KarchinLab/mhcnuggets-2.0	(183)
ConvMHC	BA	R	NN	Pan	http://jumong.kaist.ac.kr:8080/convmhc	(116)
HLA-CNN	BA	R	NN	S	https://github.com/uci-cbcl/HLA-bind	(114)
SYFPEITHI	BA + MS	R	PWM	S	http://syfpeithi.de/0-Home.htm	(106)
PSSMHCpan	BA	BA	PWM	Pan	https://github.com/BGI2016/PSSMHCpan	(184)

Column 2, BA, binding affinity; BS, binding stability; MS, HLA peptidomics data; column 3, BA, binding affinity; R, ranking; column 4, NN, Neural network (including deep networks); PWM, position weight matrices; C, consensus; column 5, S, allele specific; Pan, pan-class I.