IL299801A - An attention-based neural network for predicting peptide binding, presentation, and immunogenicity - Google Patents
An attention-based neural network for predicting peptide binding, presentation, and immunogenicityInfo
- Publication number
- IL299801A IL299801A IL299801A IL29980123A IL299801A IL 299801 A IL299801 A IL 299801A IL 299801 A IL299801 A IL 299801A IL 29980123 A IL29980123 A IL 29980123A IL 299801 A IL299801 A IL 299801A
- Authority
- IL
- Israel
- Prior art keywords
- immunogenicity
- presentation
- attention
- neural network
- peptide binding
- Prior art date
Links
Classifications
-
- 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
-
- 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
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K39/0005—Vertebrate antigens
- A61K39/0011—Cancer antigens
-
- 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
-
- 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
- G06N3/0455—Auto-encoder networks; Encoder-decoder networks
-
- 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
- G06N3/0499—Feedforward networks
-
- 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
-
- 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
-
- 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
- G16B15/30—Drug targeting using structural data; Docking or binding prediction
-
- 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
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B20/30—Detection of binding sites or motifs
-
- 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
- G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
- G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
- G16H50/20—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
Landscapes
- Engineering & Computer Science (AREA)
- Health & Medical Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Physics & Mathematics (AREA)
- Theoretical Computer Science (AREA)
- General Health & Medical Sciences (AREA)
- Medical Informatics (AREA)
- Biophysics (AREA)
- Data Mining & Analysis (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Spectroscopy & Molecular Physics (AREA)
- Chemical & Material Sciences (AREA)
- Public Health (AREA)
- Artificial Intelligence (AREA)
- Software Systems (AREA)
- Evolutionary Computation (AREA)
- Epidemiology (AREA)
- Bioinformatics & Computational Biology (AREA)
- Biotechnology (AREA)
- Evolutionary Biology (AREA)
- Biomedical Technology (AREA)
- Medicinal Chemistry (AREA)
- Pharmacology & Pharmacy (AREA)
- Molecular Biology (AREA)
- Databases & Information Systems (AREA)
- Computational Linguistics (AREA)
- Computing Systems (AREA)
- General Engineering & Computer Science (AREA)
- General Physics & Mathematics (AREA)
- Mathematical Physics (AREA)
- Computer Vision & Pattern Recognition (AREA)
- Bioethics (AREA)
- Oncology (AREA)
- Mycology (AREA)
- Veterinary Medicine (AREA)
- Animal Behavior & Ethology (AREA)
- Crystallography & Structural Chemistry (AREA)
- Immunology (AREA)
- Microbiology (AREA)
- Primary Health Care (AREA)
Applications Claiming Priority (2)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US202063053307P | 2020-07-17 | 2020-07-17 | |
| PCT/US2021/042105 WO2022016125A1 (en) | 2020-07-17 | 2021-07-16 | Attention-based neural network to predict peptide binding, presentation, and immunogenicity |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| IL299801A true IL299801A (en) | 2023-03-01 |
Family
ID=77265296
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| IL299801A IL299801A (en) | 2020-07-17 | 2021-07-16 | An attention-based neural network for predicting peptide binding, presentation, and immunogenicity |
Country Status (11)
| Country | Link |
|---|---|
| US (1) | US20220122690A1 (https=) |
| EP (2) | EP4513509A3 (https=) |
| JP (1) | JP2023534283A (https=) |
| KR (1) | KR20230042048A (https=) |
| CN (1) | CN115997254A (https=) |
| AU (1) | AU2021308081A1 (https=) |
| BR (1) | BR112023000827A2 (https=) |
| CA (1) | CA3180799A1 (https=) |
| IL (1) | IL299801A (https=) |
| MX (1) | MX2023000618A (https=) |
| WO (1) | WO2022016125A1 (https=) |
Families Citing this family (41)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN111951887B (zh) * | 2020-07-27 | 2024-06-28 | 深圳市新合生物医疗科技有限公司 | 基于深度学习的白细胞抗原与多肽结合亲和力预测方法 |
| US12190207B2 (en) * | 2020-12-22 | 2025-01-07 | Collibra Belgium Bv | System for preparing machine learning training data for use in evaluation of term definition quality |
| US20220245917A1 (en) * | 2021-02-04 | 2022-08-04 | Google Llc | Systems and methods for nearest-neighbor prediction based machine learned models |
| MX2023011119A (es) * | 2021-03-25 | 2023-10-03 | Genentech Inc | Uso de redes neuronales para predecir inmunogenicidad de peptidos. |
| CN114822680B (zh) * | 2022-02-24 | 2024-10-15 | 南京工业大学 | 一种基于对比学习的tcr与抗原复合物亲和力预测算法 |
| WO2023249440A1 (ko) * | 2022-06-24 | 2023-12-28 | 지니너스 주식회사 | 펩타이드와 t 세포 수용체간의 결합을 추정하는 방법 및 장치 |
| CN115273979B (zh) * | 2022-07-04 | 2024-09-13 | 苏州大学 | 基于自注意力机制的单核苷酸无义突变致病性预测系统 |
| CN115240786B (zh) * | 2022-08-09 | 2025-10-24 | 腾讯科技（深圳）有限公司 | 反应物分子的预测方法、训练方法、装置以及电子设备 |
| US20260074011A1 (en) * | 2022-08-26 | 2026-03-12 | Massachusetts Institute Of Technology | End-to-end machine learning-driven design of proteins |
| TW202430881A (zh) * | 2022-09-26 | 2024-08-01 | 美商柏帝斯生物科技公司 | 使用質譜數據對病況進行分類之方法及系統 |
| CN115954050B (zh) * | 2022-09-30 | 2025-05-30 | 上海天鹜科技有限公司 | 基于蛋白质工程的集成序列与结构特征的深度学习系统及预测方法 |
| CN115512396B (zh) * | 2022-11-01 | 2023-04-07 | 山东大学 | 一种基于深度神经网络的抗癌肽和抗菌肽预测方法及系统 |
| JP2025539935A (ja) | 2022-11-15 | 2025-12-10 | ジェネンテック， インコーポレイテッド | ペプチド治療薬のための多様な候補ペプチドの選択 |
| JP2026500160A (ja) * | 2022-12-05 | 2026-01-06 | ジェネンテック， インコーポレイテッド | 主要組織適合遺伝子複合体分子によるペプチド提示の予測のための方法およびシステム |
| KR20240086923A (ko) * | 2022-12-09 | 2024-06-19 | 주식회사 Lg 경영개발원 | Mhc 클래스 ii 결합 및 면역원성 예측 모델을 위한 데이터 증강 방법, 장치 및 프로그램 |
| CN115862742B (zh) * | 2022-12-15 | 2026-02-24 | 北京航空航天大学 | 基于自注意力机制的双向肽段测序方法及应用 |
| KR20240111065A (ko) * | 2023-01-09 | 2024-07-16 | 주식회사 네오젠티씨 | 인공지능 기술을 이용하여 면역원성 정보를 생성하기 위한 방법 및 장치 |
| CN116052779B (zh) * | 2023-01-16 | 2025-08-29 | 厦门大学 | 一种融合基因和序列信息的适应性免疫受体预测方法 |
| CN116959581A (zh) * | 2023-01-17 | 2023-10-27 | 腾讯科技（深圳）有限公司 | 免疫原性预测模型的训练方法、装置、设备及存储介质 |
| CN120858409A (zh) * | 2023-03-09 | 2025-10-28 | 免疫生物公司 | 用于t细胞受体（tcr）测定设计的方法和系统 |
| WO2024194208A1 (en) * | 2023-03-17 | 2024-09-26 | Achilles Therapeutics Uk Limited | Prediction of immunogenicity |
| CN116665769A (zh) * | 2023-04-27 | 2023-08-29 | 深药科技(苏州)有限公司 | T细胞受体与肽相互作用预测方法及系统 |
| EP4713958A2 (en) * | 2023-05-19 | 2026-03-25 | Enveda Therapeutics, Inc. | Predicting a mass spectrum from a chemical compound and uses thereof |
| CN116309596B (zh) * | 2023-05-23 | 2023-08-04 | 杭州华得森生物技术有限公司 | 基于微流控芯片的ctc细胞检测方法及其系统 |
| EP4478367A1 (en) * | 2023-06-13 | 2024-12-18 | NEC OncoImmunity AS | B-cell epitope prediction |
| EP4478250A1 (en) * | 2023-06-13 | 2024-12-18 | NEC OncoImmunity AS | Method of training a machine learning model |
| CN116469457B (zh) * | 2023-06-14 | 2023-10-13 | 普瑞基准科技（北京）有限公司 | Mhc与抗原多肽结合、呈递及免疫原性的预测模型训练方法和装置 |
| CN116844637B (zh) * | 2023-07-07 | 2024-02-09 | 北京分子之心科技有限公司 | 一种获取第一源抗体序列对应的第二源蛋白质序列的方法与设备 |
| CN117037902B (zh) * | 2023-07-18 | 2024-08-20 | 哈尔滨工业大学 | 基于蛋白质物理化学特征嵌入的肽与mhc i类蛋白结合基序预测方法 |
| WO2025038706A1 (en) * | 2023-08-15 | 2025-02-20 | Visa International Service Association | Transaction generative pre-trained transformer |
| KR20250058439A (ko) * | 2023-10-23 | 2025-04-30 | 주식회사 Lg 경영개발원 | 비관측 단백질 복합체를 활용하여 항원 제시 모델을 생성하는 단백질 상호 작용 예측 장치 및 이를 이용한 방법 |
| KR20250058440A (ko) * | 2023-10-23 | 2025-04-30 | 주식회사 Lg 경영개발원 | 인공지능을 기반으로 단백질 복합체 표면 정보를 통해 단백질 상호 작용을 예측하는 장치 및 이를 이용한 방법 |
| KR20250058438A (ko) * | 2023-10-23 | 2025-04-30 | 주식회사 Lg 경영개발원 | 입력 서열을 변환하기 위한 서열 변환 신경망 구현 장치 및 이를 이용한 학습 방법 |
| CN117831789B (zh) * | 2024-03-05 | 2024-05-28 | 北京市肿瘤防治研究所 | 癌症治疗反应预测系统及其控制方法 |
| WO2025191132A1 (en) * | 2024-03-15 | 2025-09-18 | Evaxion Biotech A/S | Mhc ligand identification and related systems and methods |
| US20250308627A1 (en) * | 2024-04-02 | 2025-10-02 | Nec Laboratories America, Inc. | T-cell receptor-peptide interaction prediction for medical decision making |
| WO2025216910A1 (en) * | 2024-04-08 | 2025-10-16 | Sanofi Pasteur, Inc. | Selecting a candidate antigen for a vaccine using a biological response machine learning model |
| WO2025216911A1 (en) * | 2024-04-08 | 2025-10-16 | Sanofi Pasteur, Inc. | Selecting a candidate antigen for a vaccine using a biological response machine learning model |
| WO2025226580A1 (en) | 2024-04-22 | 2025-10-30 | Genentech, Inc. | Methods and systems for hla loss determination |
| CN118484654B (zh) * | 2024-05-27 | 2025-04-29 | 黑龙江大学 | 利用机器学习获取二维纳米材料剥离能的方法 |
| CN118248218B (zh) * | 2024-05-30 | 2024-07-30 | 北京航空航天大学杭州创新研究院 | 基于AI算法开发高亲和力捕获抗体EpCAM的方法 |
Family Cites Families (6)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| DE10347710B4 (de) | 2003-10-14 | 2006-03-30 | Johannes-Gutenberg-Universität Mainz | Rekombinante Impfstoffe und deren Verwendung |
| DE102005046490A1 (de) | 2005-09-28 | 2007-03-29 | Johannes-Gutenberg-Universität Mainz | Modifikationen von RNA, die zu einer erhöhten Transkriptstabilität und Translationseffizienz führen |
| EP2281579A1 (en) | 2009-08-05 | 2011-02-09 | BioNTech AG | Vaccine composition comprising 5'-Cap modified RNA |
| WO2013143555A1 (en) | 2012-03-26 | 2013-10-03 | Biontech Ag | Rna formulation for immunotherapy |
| WO2017059902A1 (en) | 2015-10-07 | 2017-04-13 | Biontech Rna Pharmaceuticals Gmbh | 3' utr sequences for stabilization of rna |
| CN112912960B (zh) * | 2018-08-20 | 2024-10-29 | 南托米克斯有限责任公司 | 使用递归神经网络编码器和注意力加权来改进对新表位的主要组织相容性复合物(mhc)-肽结合预测的方法和系统 |
-
2021
- 2021-07-16 US US17/378,651 patent/US20220122690A1/en active Pending
- 2021-07-16 EP EP24213821.2A patent/EP4513509A3/en active Pending
- 2021-07-16 CA CA3180799A patent/CA3180799A1/en active Pending
- 2021-07-16 EP EP21752405.7A patent/EP4182924A1/en active Pending
- 2021-07-16 WO PCT/US2021/042105 patent/WO2022016125A1/en not_active Ceased
- 2021-07-16 MX MX2023000618A patent/MX2023000618A/es unknown
- 2021-07-16 BR BR112023000827A patent/BR112023000827A2/pt unknown
- 2021-07-16 KR KR1020237005289A patent/KR20230042048A/ko active Pending
- 2021-07-16 JP JP2023502978A patent/JP2023534283A/ja active Pending
- 2021-07-16 IL IL299801A patent/IL299801A/en unknown
- 2021-07-16 AU AU2021308081A patent/AU2021308081A1/en active Pending
- 2021-07-16 CN CN202180046244.1A patent/CN115997254A/zh active Pending
Also Published As
| Publication number | Publication date |
|---|---|
| EP4513509A3 (en) | 2025-05-21 |
| JP2023534283A (ja) | 2023-08-08 |
| KR20230042048A (ko) | 2023-03-27 |
| MX2023000618A (es) | 2023-04-10 |
| CN115997254A (zh) | 2023-04-21 |
| US20220122690A1 (en) | 2022-04-21 |
| EP4513509A2 (en) | 2025-02-26 |
| WO2022016125A1 (en) | 2022-01-20 |
| EP4182924A1 (en) | 2023-05-24 |
| AU2021308081A1 (en) | 2022-11-17 |
| BR112023000827A2 (pt) | 2023-02-07 |
| CA3180799A1 (en) | 2022-01-20 |
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