CA3142339A1 - Machine learning-based apparatus for engineering meso-scale peptides and methods and system for the same - Google Patents

Machine learning-based apparatus for engineering meso-scale peptides and methods and system for the same Download PDF

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Publication number
CA3142339A1
CA3142339A1 CA3142339A CA3142339A CA3142339A1 CA 3142339 A1 CA3142339 A1 CA 3142339A1 CA 3142339 A CA3142339 A CA 3142339A CA 3142339 A CA3142339 A CA 3142339A CA 3142339 A1 CA3142339 A1 CA 3142339A1
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blueprint
records
machine learning
learning model
reference target
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CA3142339A
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English (en)
French (fr)
Inventor
Matthew P. Greving
Alexander T. TAGUCHI
Kevin Eduard HAUSER
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Ibio Inc
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Rubryc Therapeutics Inc
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Publication of CA3142339A1 publication Critical patent/CA3142339A1/en
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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
    • 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
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • 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
    • 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
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N20/00—Machine learning
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N20/00—Machine learning
    • G06N20/10—Machine learning using kernel methods, e.g. support vector machines [SVM]
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N20/00—Machine learning
    • G06N20/20—Ensemble learning
    • 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]
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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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  • Engineering & Computer Science (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Theoretical Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • 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)
  • Databases & Information Systems (AREA)
  • Epidemiology (AREA)
  • Public Health (AREA)
CA3142339A 2019-05-31 2020-05-13 Machine learning-based apparatus for engineering meso-scale peptides and methods and system for the same Pending CA3142339A1 (en)

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

Publications (1)

Publication Number Publication Date
CA3142339A1 true CA3142339A1 (en) 2020-12-03

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CA3142339A Pending CA3142339A1 (en) 2019-05-31 2020-05-13 Machine learning-based apparatus for engineering meso-scale peptides and methods and system for the same
CA3142227A Pending CA3142227A1 (en) 2019-05-31 2020-05-13 Meso-scale engineered peptides and methods of selecting

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Country Status (7)

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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=)

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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

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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
JP7579812B2 (ja) 2024-11-08
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
WO2020242766A1 (en) 2020-12-03
EP3976083A1 (en) 2022-04-06

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