Title:
AMINO ACID SEQUENCE SEARCHING DEVICE, VACCINE, AMINO ACID SEQUENCE SEARCHING METHOD, AND AMINO ACID SEQUENCE SEARCHING PROGRAM
Document Type and Number:
WIPO Patent Application WO/2021/106706
Kind Code:
A1
Abstract:
The present invention improves the accuracy of searching for an amino acid sequence of interest. An information processing device (amino acid sequence searching device) 1 is provided with: a storage unit 17 that stores a trained model for amino acid sequence binding prediction that has been trained with the series data structure of amino acid sequence data for a plurality of items of amino acid sequence data by using a deep learning model with an attention mechanism; a first input unit 11 and a second input unit 13 that input first amino acid sequence data and second amino acid sequence data, respectively; and a searching unit 16 that uses the trained model read from the storage unit 17 to output binding prediction information pertaining to whether the first amino acid sequence data binds as part of the second amino acid sequence data or not.
Inventors:
FUJITA HARUKA (JP)
SADAMITSU KUGATSU (JP)
SAKAGUCHI MAKOTO (JP)
TENMA AKIKO (JP)
NAKAGAMI HIRONORI (JP)
MORISHITA RYUICHI (JP)
SADAMITSU KUGATSU (JP)
SAKAGUCHI MAKOTO (JP)
TENMA AKIKO (JP)
NAKAGAMI HIRONORI (JP)
MORISHITA RYUICHI (JP)
Application Number:
PCT/JP2020/042958
Publication Date:
June 03, 2021
Filing Date:
November 18, 2020
Export Citation:
Assignee:
FUTURE CORP (JP)
FUNPEP CO LTD (JP)
UNIV OSAKA (JP)
FUNPEP CO LTD (JP)
UNIV OSAKA (JP)
International Classes:
G16B40/20; C07K2/00; C07K14/00; G06N3/04; G16B15/30
Foreign References:
| US20190303535A1 | 2019-10-03 |
Other References:
LIU ZHONGHAO, JIN JING, CUI YUXIN, XIONG ZHENG, NASIRI ALIREZA, ZHAO YONG, HU JIANJUN: "DeepSeqPanII: an interpretable recurrent neural network model with attention mechanism for peptide-HLA class II binding prediction", IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, IEEE SERVICE CENTER, NEW YORK, NY., US, vol. 14, 1 January 2021 (2021-01-01), US, pages 1 - 1, XP055830651, ISSN: 1545-5963, DOI: 10.1109/TCBB.2021.3074927
HARINDER SINGH, ANSARI HIFZUR RAHMAN, RAGHAVA GAJENDRA P. S.: "Improved Method for Linear B-Cell Epitope Prediction Using Antigen’s Primary Sequence", PLOS ONE, vol. 8, no. 5, 1 January 2013 (2013-01-01), pages 1 - 8, XP055242468, DOI: 10.1371/journal.pone.0062216
TSUBAKI MASASHI, TOMII KENTARO, SESE JUN: "Compound–protein interaction prediction with end-to-end learning of neural networks for graphs and sequences", BIOINFORMATICS, OXFORD UNIVERSITY PRESS , SURREY, GB, vol. 35, no. 2, 15 January 2019 (2019-01-15), GB, pages 309 - 318, XP055826403, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/bty535
JIN JING, LIU ZHONGHAO, NASIRI ALIREZA, CUI YUXIN, LOUIS STEPHEN, ZHANG ANSI, ZHAO YONG, HU JIANJUN: "Attention mechanism-based deep learning pan-specific model for interpretable MHC-I peptide binding prediction", BIORXIV, 7 November 2019 (2019-11-07), XP055830649, Retrieved from the Internet [retrieved on 20210806], DOI: 10.1101/830737
JESPERSEN MARTIN CLOSTER, PETERS BJOERN, NIELSEN MORTEN, MARCATILI PAOLO: "BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes", NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, GB, vol. 45, no. W1, 3 July 2017 (2017-07-03), GB, pages W24 - W29, XP055830648, ISSN: 0305-1048, DOI: 10.1093/nar/gkx346
HARINDER SINGH, ANSARI HIFZUR RAHMAN, RAGHAVA GAJENDRA P. S.: "Improved Method for Linear B-Cell Epitope Prediction Using Antigen’s Primary Sequence", PLOS ONE, vol. 8, no. 5, 1 January 2013 (2013-01-01), pages 1 - 8, XP055242468, DOI: 10.1371/journal.pone.0062216
TSUBAKI MASASHI, TOMII KENTARO, SESE JUN: "Compound–protein interaction prediction with end-to-end learning of neural networks for graphs and sequences", BIOINFORMATICS, OXFORD UNIVERSITY PRESS , SURREY, GB, vol. 35, no. 2, 15 January 2019 (2019-01-15), GB, pages 309 - 318, XP055826403, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/bty535
JIN JING, LIU ZHONGHAO, NASIRI ALIREZA, CUI YUXIN, LOUIS STEPHEN, ZHANG ANSI, ZHAO YONG, HU JIANJUN: "Attention mechanism-based deep learning pan-specific model for interpretable MHC-I peptide binding prediction", BIORXIV, 7 November 2019 (2019-11-07), XP055830649, Retrieved from the Internet
JESPERSEN MARTIN CLOSTER, PETERS BJOERN, NIELSEN MORTEN, MARCATILI PAOLO: "BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes", NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, GB, vol. 45, no. W1, 3 July 2017 (2017-07-03), GB, pages W24 - W29, XP055830648, ISSN: 0305-1048, DOI: 10.1093/nar/gkx346
Attorney, Agent or Firm:
MIYOSHI Hidekazu et al. (JP)
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