PMID- 33886473
OWN - NLM
STAT- MEDLINE
DCOM- 20220810
LR  - 20220827
IS  - 1557-9964 (Electronic)
IS  - 1545-5963 (Linking)
VI  - 19
IP  - 4
DP  - 2022 Jul-Aug
TI  - DeepSeqPanII: An Interpretable Recurrent Neural Network Model With Attention 
      Mechanism for Peptide-HLA Class II Binding Prediction.
PG  - 2188-2196
LID - 10.1109/TCBB.2021.3074927 [doi]
AB  - Human leukocyte antigen (HLA) complex molecules play an essential role in immune 
      interactions by presenting peptides on the cell surface to T cells. With 
      significant deep learning progress, a series of neural network-based models have 
      been proposed and demonstrated with their excellent performances for peptide-HLA 
      class I binding prediction. However, there is still a lack of effective binding 
      prediction models for HLA class II protein binding with peptides due to its 
      inherent challenges. We present a novel sequence-based pan-specific neural 
      network structure, DeepSeaPanII, for peptide-HLA class II binding prediction in 
      this work. Our model is an end-to-end neural network model without the need for 
      pre-or post-processing on input samples compared with existing pan-specific 
      models. Besides state-of-the-art performance in binding affinity prediction, 
      DeepSeqPanII can also extract biological insight on the binding mechanism over 
      the peptide by its attention mechanism-based binding core prediction capability. 
      The leave-one-allele-out cross-validation and benchmark evaluation results show 
      that our proposed network model achieved state-of-the-art performance in HLA-II 
      peptide binding. The source code and trained models are freely available at 
      https://github.com/pcpLiu/DeepSeqPanII.
FAU - Liu, Zhonghao
AU  - Liu Z
FAU - Jin, Jing
AU  - Jin J
FAU - Cui, Yuxin
AU  - Cui Y
FAU - Xiong, Zheng
AU  - Xiong Z
FAU - Nasiri, Alireza
AU  - Nasiri A
FAU - Zhao, Yong
AU  - Zhao Y
FAU - Hu, Jianjun
AU  - Hu J
LA  - eng
GR  - R01 AI127203/AI/NIAID NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20220808
PL  - United States
TA  - IEEE/ACM Trans Comput Biol Bioinform
JT  - IEEE/ACM transactions on computational biology and bioinformatics
JID - 101196755
RN  - 0 (HLA Antigens)
RN  - 0 (Histocompatibility Antigens Class I)
RN  - 0 (Peptides)
SB  - IM
MH  - *HLA Antigens/metabolism
MH  - Histocompatibility Antigens Class I/chemistry/metabolism
MH  - Humans
MH  - *Neural Networks, Computer
MH  - Peptides/chemistry/genetics
MH  - Protein Binding
EDAT- 2021/04/23 06:00
MHDA- 2022/08/11 06:00
CRDT- 2021/04/22 17:22
PHST- 2021/04/23 06:00 [pubmed]
PHST- 2022/08/11 06:00 [medline]
PHST- 2021/04/22 17:22 [entrez]
AID - 10.1109/TCBB.2021.3074927 [doi]
PST - ppublish
SO  - IEEE/ACM Trans Comput Biol Bioinform. 2022 Jul-Aug;19(4):2188-2196. doi: 
      10.1109/TCBB.2021.3074927. Epub 2022 Aug 8.