KR20230042048A - 펩타이드 결합, 제시, 및 면역원성을 예측하기 위한 어텐션-기반 신경망 - Google Patents

펩타이드 결합, 제시, 및 면역원성을 예측하기 위한 어텐션-기반 신경망 Download PDF

Info

Publication number
KR20230042048A
KR20230042048A KR1020237005289A KR20237005289A KR20230042048A KR 20230042048 A KR20230042048 A KR 20230042048A KR 1020237005289 A KR1020237005289 A KR 1020237005289A KR 20237005289 A KR20237005289 A KR 20237005289A KR 20230042048 A KR20230042048 A KR 20230042048A
Authority
KR
South Korea
Prior art keywords
peptide
sequence
attention
ipc
mhc
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
KR1020237005289A
Other languages
English (en)
Korean (ko)
Inventor
카이 리우
니콜라스 윈스톤 로운스베리
윌리엄 존 트리프트
앤드릭 쿠에이드 브로드웰
렐리아 이본느 델라마르
수치트 수실 준준왈라
Original Assignee
제넨테크, 인크.
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by 제넨테크, 인크. filed Critical 제넨테크, 인크.
Publication of KR20230042048A publication Critical patent/KR20230042048A/ko
Pending legal-status Critical Current

Links

Images

Classifications

    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20Supervised data analysis
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00Medicinal preparations containing antigens or antibodies
    • A61K39/0005Vertebrate antigens
    • A61K39/0011Cancer antigens
    • GPHYSICS
    • G06COMPUTING OR CALCULATING; COUNTING
    • G06NCOMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00Computing arrangements based on biological models
    • G06N3/02Neural networks
    • G06N3/04Architecture, e.g. interconnection topology
    • GPHYSICS
    • G06COMPUTING OR CALCULATING; COUNTING
    • G06NCOMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00Computing arrangements based on biological models
    • G06N3/02Neural networks
    • G06N3/04Architecture, e.g. interconnection topology
    • G06N3/045Combinations of networks
    • G06N3/0455Auto-encoder networks; Encoder-decoder networks
    • GPHYSICS
    • G06COMPUTING OR CALCULATING; COUNTING
    • G06NCOMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00Computing arrangements based on biological models
    • G06N3/02Neural networks
    • G06N3/04Architecture, e.g. interconnection topology
    • G06N3/0499Feedforward networks
    • GPHYSICS
    • G06COMPUTING OR CALCULATING; COUNTING
    • G06NCOMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00Computing arrangements based on biological models
    • G06N3/02Neural networks
    • G06N3/08Learning methods
    • GPHYSICS
    • G06COMPUTING OR CALCULATING; COUNTING
    • G06NCOMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00Computing arrangements based on biological models
    • G06N3/02Neural networks
    • G06N3/08Learning methods
    • G06N3/09Supervised learning
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B15/00ICT specially adapted for analysing two-dimensional [2D] or three-dimensional [3D] molecular structures, e.g. structural or functional relations or structure alignment
    • G16B15/30Drug targeting using structural data; Docking or binding prediction
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/30Detection of binding sites or motifs
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16HHEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/20ICT 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)
KR1020237005289A 2020-07-17 2021-07-16 펩타이드 결합, 제시, 및 면역원성을 예측하기 위한 어텐션-기반 신경망 Pending KR20230042048A (ko)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US202063053307P 2020-07-17 2020-07-17
US63/053,307 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
KR20230042048A true KR20230042048A (ko) 2023-03-27

Family

ID=77265296

Family Applications (1)

Application Number Title Priority Date Filing Date
KR1020237005289A Pending KR20230042048A (ko) 2020-07-17 2021-07-16 펩타이드 결합, 제시, 및 면역원성을 예측하기 위한 어텐션-기반 신경망

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)

* Cited by examiner, † Cited by third party
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)

* Cited by examiner, † Cited by third party
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

Also Published As

Publication number Publication date
EP4513509A3 (en) 2025-05-21
JP2023534283A (ja) 2023-08-08
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
IL299801A (en) 2023-03-01
EP4182924A1 (en) 2023-05-24
AU2021308081A1 (en) 2022-11-17
BR112023000827A2 (pt) 2023-02-07
CA3180799A1 (en) 2022-01-20

Similar Documents

Publication Publication Date Title
KR20230042048A (ko) 펩타이드 결합, 제시, 및 면역원성을 예측하기 위한 어텐션-기반 신경망
CN112771214B (zh) 用于选择新表位的方法
CN110752041B (zh) 基于二代测序的新生抗原预测方法、装置和存储介质
CN114333999B (zh) 一种分子组学与计算结构联用的肿瘤新生抗原检测筛选方法及系统
CA3217623A1 (en) Compositions and method for optimized peptide vaccines using residue optimization
Zhang et al. Epitope-anchored contrastive transfer learning for paired CD8+ T cell receptor–antigen recognition
AU2019382854B2 (en) Method and system of targeting epitopes for neoantigen-based immunotherapy
CN109072227A (zh) 用于免疫治疗的监测和诊断及治疗剂的设计
US20240021274A1 (en) Using neural networks to predict peptide immunogenicity
Tabibpour et al. Putative novel outer membrane antigens multi-epitope DNA vaccine candidates identified by Immunoinformatic approaches to control Acinetobacter baumannii
US20260018244A1 (en) Methods and systems for prediction of peptide presentation by major histocompatibility complex molecules
Tarabini et al. Mutations in glioblastoma proteins do not disrupt epitope presentation and recognition, maintaining a specific CD8 T cell immune response potential
EP4437544A1 (en) Methods for predicting immunogenicity of mutations or neoantigenic peptides in tumors
HK40101009A (zh) 使用神经网络预测肽免疫原性
US20250273291A1 (en) Selection of diverse candidate peptides for peptide therapeutics
KR20260045308A (ko) 바인딩 및 면역원성 정보를 이용한 hla-펩타이드 상호작용 예측 방법
KR20240021885A (ko) Rna 돌연변이 발현의 정량화
HK40052691B (en) Method and system of targeting epitopes for neoantigen-based immunotherapy

Legal Events

Date Code Title Description
PA0105 International application

Patent event date: 20230214

Patent event code: PA01051R01D

Comment text: International Patent Application

PG1501 Laying open of application
A201 Request for examination
PA0201 Request for examination

Patent event code: PA02012R01D

Patent event date: 20240715

Comment text: Request for Examination of Application