JP7579812B2 - メソスケールペプチドを操作するための機械学習ベースの装置およびそのための方法およびシステム - Google Patents
メソスケールペプチドを操作するための機械学習ベースの装置およびそのための方法およびシステム Download PDFInfo
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- JP7579812B2 JP7579812B2 JP2021571033A JP2021571033A JP7579812B2 JP 7579812 B2 JP7579812 B2 JP 7579812B2 JP 2021571033 A JP2021571033 A JP 2021571033A JP 2021571033 A JP2021571033 A JP 2021571033A JP 7579812 B2 JP7579812 B2 JP 7579812B2
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
- G16B40/20—Supervised data analysis
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
- C07K1/10—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length using coupling agents
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K14/001—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof by chemical synthesis
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
- G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
- G01N33/6845—Methods of identifying protein-protein interactions in protein mixtures
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- G—PHYSICS
- G06—COMPUTING OR CALCULATING; COUNTING
- G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
- G06N20/00—Machine learning
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- G—PHYSICS
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- G06N20/00—Machine learning
- G06N20/10—Machine learning using kernel methods, e.g. support vector machines [SVM]
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- G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
- G06N20/00—Machine learning
- G06N20/20—Ensemble learning
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- G—PHYSICS
- G06—COMPUTING OR CALCULATING; COUNTING
- G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
- G06N3/00—Computing arrangements based on biological models
- G06N3/02—Neural networks
- G06N3/04—Architecture, e.g. interconnection topology
- G06N3/044—Recurrent networks, e.g. Hopfield networks
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- G—PHYSICS
- G06—COMPUTING OR CALCULATING; COUNTING
- G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
- G06N3/00—Computing arrangements based on biological models
- G06N3/02—Neural networks
- G06N3/04—Architecture, e.g. interconnection topology
- G06N3/045—Combinations of networks
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- G—PHYSICS
- G06—COMPUTING OR CALCULATING; COUNTING
- G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
- G06N3/00—Computing arrangements based on biological models
- G06N3/02—Neural networks
- G06N3/04—Architecture, e.g. interconnection topology
- G06N3/0464—Convolutional networks [CNN, ConvNet]
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- G—PHYSICS
- G06—COMPUTING OR CALCULATING; COUNTING
- G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
- G06N3/00—Computing arrangements based on biological models
- G06N3/02—Neural networks
- G06N3/04—Architecture, e.g. interconnection topology
- G06N3/0475—Generative networks
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- G—PHYSICS
- G06—COMPUTING OR CALCULATING; COUNTING
- G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
- G06N3/00—Computing arrangements based on biological models
- G06N3/02—Neural networks
- G06N3/08—Learning methods
- G06N3/09—Supervised learning
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- G—PHYSICS
- G06—COMPUTING OR CALCULATING; COUNTING
- G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
- G06N5/00—Computing arrangements using knowledge-based models
- G06N5/01—Dynamic search techniques; Heuristics; Dynamic trees; Branch-and-bound
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- G—PHYSICS
- G06—COMPUTING OR CALCULATING; COUNTING
- G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
- G06N5/00—Computing arrangements using knowledge-based models
- G06N5/04—Inference or reasoning models
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B15/00—ICT specially adapted for analysing two-dimensional [2D] or three-dimensional [3D] molecular structures, e.g. structural or functional relations or structure alignment
- G16B15/20—Protein or domain folding
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
- G16B5/30—Dynamic-time models
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- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
- Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
- Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
- Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation
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- Molecular Biology (AREA)
- Software Systems (AREA)
- General Health & Medical Sciences (AREA)
- Biophysics (AREA)
- Data Mining & Analysis (AREA)
- Evolutionary Computation (AREA)
- Artificial Intelligence (AREA)
- General Physics & Mathematics (AREA)
- Medical Informatics (AREA)
- Computing Systems (AREA)
- Mathematical Physics (AREA)
- General Engineering & Computer Science (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Bioinformatics & Computational Biology (AREA)
- Biotechnology (AREA)
- Spectroscopy & Molecular Physics (AREA)
- Biomedical Technology (AREA)
- Computational Linguistics (AREA)
- Organic Chemistry (AREA)
- Evolutionary Biology (AREA)
- Computer Vision & Pattern Recognition (AREA)
- Medicinal Chemistry (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Biochemistry (AREA)
- Genetics & Genomics (AREA)
- Immunology (AREA)
- Hematology (AREA)
- Urology & Nephrology (AREA)
- Physiology (AREA)
- Gastroenterology & Hepatology (AREA)
- Analytical Chemistry (AREA)
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Priority Applications (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| JP2024189173A JP2025016594A (ja) | 2019-05-31 | 2024-10-28 | メソスケールペプチドを操作するための機械学習ベースの装置およびそのための方法およびシステム |
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US201962855767P | 2019-05-31 | 2019-05-31 | |
| US62/855,767 | 2019-05-31 | ||
| PCT/US2020/032724 WO2020242766A1 (en) | 2019-05-31 | 2020-05-13 | Machine learning-based apparatus for engineering meso-scale peptides and methods and system for the same |
Related Child Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| JP2024189173A Division JP2025016594A (ja) | 2019-05-31 | 2024-10-28 | メソスケールペプチドを操作するための機械学習ベースの装置およびそのための方法およびシステム |
Publications (3)
| Publication Number | Publication Date |
|---|---|
| JP2022535769A JP2022535769A (ja) | 2022-08-10 |
| JP2022535769A5 JP2022535769A5 (https=) | 2023-06-15 |
| JP7579812B2 true JP7579812B2 (ja) | 2024-11-08 |
Family
ID=73553528
Family Applications (4)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| JP2021571033A Active JP7579812B2 (ja) | 2019-05-31 | 2020-05-13 | メソスケールペプチドを操作するための機械学習ベースの装置およびそのための方法およびシステム |
| JP2021570755A Pending JP2022535511A (ja) | 2019-05-31 | 2020-05-13 | メソスケール操作されたペプチドおよび選択方法 |
| JP2024189173A Pending JP2025016594A (ja) | 2019-05-31 | 2024-10-28 | メソスケールペプチドを操作するための機械学習ベースの装置およびそのための方法およびシステム |
| JP2025077381A Pending JP2025118804A (ja) | 2019-05-31 | 2025-05-07 | メソスケール操作されたペプチドおよび選択方法 |
Family Applications After (3)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| JP2021570755A Pending JP2022535511A (ja) | 2019-05-31 | 2020-05-13 | メソスケール操作されたペプチドおよび選択方法 |
| JP2024189173A Pending JP2025016594A (ja) | 2019-05-31 | 2024-10-28 | メソスケールペプチドを操作するための機械学習ベースの装置およびそのための方法およびシステム |
| JP2025077381A Pending JP2025118804A (ja) | 2019-05-31 | 2025-05-07 | メソスケール操作されたペプチドおよび選択方法 |
Country Status (7)
| Country | Link |
|---|---|
| US (3) | US11545238B2 (https=) |
| EP (2) | EP3977117A4 (https=) |
| JP (4) | JP7579812B2 (https=) |
| KR (3) | KR20260028069A (https=) |
| CN (2) | CN114585918A (https=) |
| CA (2) | CA3142339A1 (https=) |
| WO (2) | WO2020242765A1 (https=) |
Families Citing this family (14)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| EP3880698A4 (en) | 2018-11-14 | 2022-11-30 | RubrYc Therapeutics, Inc. | MANIPULATED CD25 POLYPEPTIDES AND USES THEREOF |
| WO2022243940A1 (en) * | 2021-05-21 | 2022-11-24 | Peptone, Ltd. | Spacio-temporal determination of polypeptide structure |
| CN114065620B (zh) * | 2021-11-11 | 2022-06-03 | 四川大学 | 基于像素图表征和cnn的可解释性分子动力学轨迹分析方法 |
| US20250299780A1 (en) * | 2022-05-06 | 2025-09-25 | Dyno Therapeutics, Inc. | System and methods for predicting features of biological sequences |
| CN115512763B (zh) * | 2022-09-06 | 2023-10-24 | 北京百度网讯科技有限公司 | 多肽序列的生成方法、多肽生成模型的训练方法和装置 |
| CN116343922B (zh) * | 2022-12-31 | 2026-01-09 | 浙江大学杭州国际科创中心 | 一种基于机器学习对多肽进行预测的方法 |
| CN115881220B (zh) * | 2023-02-15 | 2023-06-06 | 北京深势科技有限公司 | 一种抗体结构预测的处理方法和装置 |
| US12587274B2 (en) | 2023-03-28 | 2026-03-24 | Quantum Generative Materials Llc | Satellite optimization management system based on natural language input and artificial intelligence |
| CN116467894B (zh) * | 2023-05-16 | 2024-08-20 | 郑州大学 | 一种基于机器学习分子动力学的辐照损伤仿真系统及方法 |
| TWI860054B (zh) * | 2023-08-22 | 2024-10-21 | 國立清華大學 | 訓練機器學習模型的方法、裝置和電腦程式產品 |
| CN116913395B (zh) * | 2023-09-13 | 2023-11-28 | 青岛虹竹生物科技有限公司 | 一种构建小分子肽数据库的数字化方法 |
| WO2025057424A1 (ja) * | 2023-09-15 | 2025-03-20 | 富士通株式会社 | 情報処理プログラム,情報処理装置および情報処理方法 |
| US12603701B2 (en) | 2023-12-27 | 2026-04-14 | Quantum Generative Materials Llc | Distributed satellite constellation management and control system |
| US12368503B2 (en) | 2023-12-27 | 2025-07-22 | Quantum Generative Materials Llc | Intent-based satellite transmit management based on preexisting historical location and machine learning |
Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| JP2002536301A (ja) | 1999-01-27 | 2002-10-29 | ザ スクリプス リサーチ インスティテュート | タンパク質モデリングツール |
| JP2010113473A (ja) | 2008-11-05 | 2010-05-20 | Saitama Univ | ペプチドとタンパク質の結合部位を予測する方法、装置、およびプログラム |
| US20130090265A1 (en) | 2011-10-11 | 2013-04-11 | Biolauncher Ltd. | Systems and methods for generation of context-specific, molecular field-based amino acid substitution matrices |
Family Cites Families (18)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| AUPP660698A0 (en) * | 1998-10-21 | 1998-11-12 | University Of Queensland, The | A method of protein engineering |
| IL147031A0 (en) * | 1999-08-02 | 2002-08-14 | Synt Em Sa | Computational design methods for making molecular mimetics |
| ATE385811T1 (de) * | 2000-12-19 | 2008-03-15 | Palatin Technologies Inc | Identifizierung zielgerichteter faltungsstellen in peptiden und proteinen |
| EP1503321A3 (en) * | 2001-08-10 | 2006-08-30 | Xencor, Inc. | Protein design automation for protein libraries |
| US20060020396A1 (en) * | 2002-09-09 | 2006-01-26 | Rene Gantier | Rational directed protein evolution using two-dimensional rational mutagenesis scanning |
| US20070192033A1 (en) | 2006-02-16 | 2007-08-16 | Microsoft Corporation | Molecular interaction predictors |
| US8050870B2 (en) | 2007-01-12 | 2011-11-01 | Microsoft Corporation | Identifying associations using graphical models |
| US8374828B1 (en) * | 2007-12-24 | 2013-02-12 | The University Of North Carolina At Charlotte | Computer implemented system for protein and drug target design utilizing quantified stability and flexibility relationships to control function |
| JP2013541528A (ja) * | 2010-09-21 | 2013-11-14 | マサチューセッツ インスティテュート オブ テクノロジー | ヒト適応haポリペプチド、ワクチン、およびインフルエンザの処置 |
| US10431325B2 (en) | 2012-08-03 | 2019-10-01 | Novartis Ag | Methods to identify amino acid residues involved in macromolecular binding and uses therefor |
| EP3417874B1 (en) * | 2012-11-28 | 2024-09-11 | BioNTech SE | Individualized vaccines for cancer |
| US10665324B2 (en) * | 2014-07-07 | 2020-05-26 | Yeda Research And Development Co. Ltd. | Method of computational protein design |
| RS61907B1 (sr) * | 2015-04-06 | 2021-06-30 | Subdomain Llc | Polipeptidi koji sadrže de novo vezujući domen i njihova primena |
| US20180068054A1 (en) * | 2016-09-06 | 2018-03-08 | University Of Washington | Hyperstable Constrained Peptides and Their Design |
| WO2018132752A1 (en) | 2017-01-13 | 2018-07-19 | Massachusetts Institute Of Technology | Machine learning based antibody design |
| WO2018201020A1 (en) * | 2017-04-28 | 2018-11-01 | University Of Washington | Folded and protease-resistant polypeptides |
| EP3880698A4 (en) * | 2018-11-14 | 2022-11-30 | RubrYc Therapeutics, Inc. | MANIPULATED CD25 POLYPEPTIDES AND USES THEREOF |
| KR20240091046A (ko) | 2018-12-21 | 2024-06-21 | 바이오엔테크 유에스 인크. | Hla 클래스 ii-특이적 에피토프 예측 및 cd4+ t 세포 특징화를 위한 방법 및 시스템 |
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2020
- 2020-05-13 JP JP2021571033A patent/JP7579812B2/ja active Active
- 2020-05-13 JP JP2021570755A patent/JP2022535511A/ja active Pending
- 2020-05-13 CA CA3142339A patent/CA3142339A1/en active Pending
- 2020-05-13 EP EP20813167.2A patent/EP3977117A4/en active Pending
- 2020-05-13 KR KR1020267002109A patent/KR20260028069A/ko active Pending
- 2020-05-13 KR KR1020217043265A patent/KR20220041784A/ko not_active Ceased
- 2020-05-13 EP EP20815607.5A patent/EP3976083A4/en active Pending
- 2020-05-13 CA CA3142227A patent/CA3142227A1/en active Pending
- 2020-05-13 WO PCT/US2020/032715 patent/WO2020242765A1/en not_active Ceased
- 2020-05-13 KR KR1020217043264A patent/KR20220039659A/ko active Pending
- 2020-05-13 WO PCT/US2020/032724 patent/WO2020242766A1/en not_active Ceased
- 2020-05-13 CN CN202080050892.XA patent/CN114585918A/zh active Pending
- 2020-05-13 CN CN202080050301.9A patent/CN114401734B/zh active Active
- 2020-12-01 US US17/108,958 patent/US11545238B2/en active Active
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2021
- 2021-11-29 US US17/537,215 patent/US20220081472A1/en active Pending
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2022
- 2022-10-07 US US17/961,942 patent/US20230095685A1/en active Pending
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2024
- 2024-10-28 JP JP2024189173A patent/JP2025016594A/ja active Pending
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2025
- 2025-05-07 JP JP2025077381A patent/JP2025118804A/ja active Pending
Patent Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| JP2002536301A (ja) | 1999-01-27 | 2002-10-29 | ザ スクリプス リサーチ インスティテュート | タンパク質モデリングツール |
| JP2010113473A (ja) | 2008-11-05 | 2010-05-20 | Saitama Univ | ペプチドとタンパク質の結合部位を予測する方法、装置、およびプログラム |
| US20130090265A1 (en) | 2011-10-11 | 2013-04-11 | Biolauncher Ltd. | Systems and methods for generation of context-specific, molecular field-based amino acid substitution matrices |
Also Published As
| Publication number | Publication date |
|---|---|
| CN114585918A (zh) | 2022-06-03 |
| US20230095685A1 (en) | 2023-03-30 |
| WO2020242765A1 (en) | 2020-12-03 |
| JP2025118804A (ja) | 2025-08-13 |
| KR20220039659A (ko) | 2022-03-29 |
| CN114401734A (zh) | 2022-04-26 |
| JP2022535769A (ja) | 2022-08-10 |
| US20210166788A1 (en) | 2021-06-03 |
| US11545238B2 (en) | 2023-01-03 |
| CA3142227A1 (en) | 2020-12-03 |
| JP2022535511A (ja) | 2022-08-09 |
| KR20220041784A (ko) | 2022-04-01 |
| CN114401734B (zh) | 2025-06-03 |
| KR20260028069A (ko) | 2026-03-03 |
| JP2025016594A (ja) | 2025-02-04 |
| EP3976083A4 (en) | 2023-07-12 |
| EP3977117A4 (en) | 2023-08-16 |
| EP3977117A1 (en) | 2022-04-06 |
| US20220081472A1 (en) | 2022-03-17 |
| CA3142339A1 (en) | 2020-12-03 |
| WO2020242766A1 (en) | 2020-12-03 |
| EP3976083A1 (en) | 2022-04-06 |
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