CA3092098C - Determining protein structure and properties based on sequence - Google Patents

Determining protein structure and properties based on sequence Download PDF

Info

Publication number
CA3092098C
CA3092098C CA3092098A CA3092098A CA3092098C CA 3092098 C CA3092098 C CA 3092098C CA 3092098 A CA3092098 A CA 3092098A CA 3092098 A CA3092098 A CA 3092098A CA 3092098 C CA3092098 C CA 3092098C
Authority
CA
Canada
Prior art keywords
proteins
protein
structural features
additional
machine learning
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.)
Active
Application number
CA3092098A
Other languages
English (en)
French (fr)
Other versions
CA3092098A1 (en
Inventor
Tileli AMIMEUR
Jeremy Martin Shaver
Randal R. Ketchem
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Just Evotec Biologics Inc
Original Assignee
Just Evotec Biologics Inc
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 Just Evotec Biologics Inc filed Critical Just Evotec Biologics Inc
Publication of CA3092098A1 publication Critical patent/CA3092098A1/en
Application granted granted Critical
Publication of CA3092098C publication Critical patent/CA3092098C/en
Active legal-status Critical Current
Anticipated expiration legal-status Critical

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
    • 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

Landscapes

  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Biophysics (AREA)
  • Theoretical Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Physiology (AREA)
  • Molecular Biology (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
CA3092098A 2018-02-26 2019-02-26 Determining protein structure and properties based on sequence Active CA3092098C (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201862635529P 2018-02-26 2018-02-26
US62/635,529 2018-02-26
PCT/US2019/019688 WO2019165476A1 (en) 2018-02-26 2019-02-26 Determining protein structure and properties based on sequence

Publications (2)

Publication Number Publication Date
CA3092098A1 CA3092098A1 (en) 2019-08-29
CA3092098C true CA3092098C (en) 2023-07-11

Family

ID=65995830

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3092098A Active CA3092098C (en) 2018-02-26 2019-02-26 Determining protein structure and properties based on sequence

Country Status (5)

Country Link
US (1) US20210043272A1 (https=)
EP (1) EP3759714A1 (https=)
JP (1) JP7482782B2 (https=)
CA (1) CA3092098C (https=)
WO (1) WO2019165476A1 (https=)

Families Citing this family (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN114974397B (zh) * 2021-02-23 2025-11-28 腾讯科技（深圳）有限公司 蛋白质结构预测模型的训练方法和蛋白质结构预测方法
CN118402005A (zh) * 2021-08-31 2024-07-26 贾斯特-埃沃泰克生物制品有限公司 用于生成蛋白质序列的残差人工神经网络
US20230217956A1 (en) 2022-01-10 2023-07-13 Climax Foods Inc. Compositions and methods for phosphorylated consumables
CN118511224A (zh) * 2022-01-21 2024-08-16 索尼集团公司 信息处理装置、信息处理方法和程序
GB202303808D0 (en) 2023-03-15 2023-04-26 Nuclera Nucleics Ltd System and method for protein sequence screening
KR102846206B1 (ko) * 2023-09-27 2025-08-18 주식회사 에이인비 표적 단백질의 단백질 응집성 추정 방법 및 장치
WO2025076393A1 (en) * 2023-10-06 2025-04-10 Genentech, Inc. Machine learning enabled estimation of differences between protein sequences

Family Cites Families (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
NZ510230A (en) 1998-08-25 2004-01-30 Scripps Research Inst Predicting protein function by electronic comparison of functional site descriptors
WO2002034876A2 (en) * 2000-09-27 2002-05-02 Affinium Pharmaceuticals, Inc. Protein data analysis
US6832162B2 (en) * 2001-02-16 2004-12-14 The Trustees Of Princeton University Methods of ab initio prediction of α helices, β sheets, and polypeptide tertiary structures
JP5509421B2 (ja) 2009-12-22 2014-06-04 独立行政法人産業技術総合研究所 可溶性予測装置および可溶性予測方法
KR101681426B1 (ko) * 2015-05-08 2016-12-12 숙명여자대학교산학협력단 위치 지향성 단백질 소수성 분석방법

Also Published As

Publication number Publication date
JP2021521503A (ja) 2021-08-26
JP7482782B2 (ja) 2024-05-14
US20210043272A1 (en) 2021-02-11
WO2019165476A1 (en) 2019-08-29
EP3759714A1 (en) 2021-01-06
CA3092098A1 (en) 2019-08-29

Similar Documents

Publication Publication Date Title
CA3092098C (en) Determining protein structure and properties based on sequence
Jin et al. CAPLA: improved prediction of protein–ligand binding affinity by a deep learning approach based on a cross-attention mechanism
Avsec et al. Effective gene expression prediction from sequence by integrating long-range interactions
Butt et al. Predicting membrane proteins and their types by extracting various sequence features into Chou’s general PseAAC
Stacey et al. A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE)
Lin et al. A combinatorial approach to the peptide feature matching problem for label-free quantification
US20220108054A1 (en) System for universal hardware-neural network architecture search (co-design)
US20230245718A1 (en) Denoising ATAC-Seq Data With Deep Learning
Ayoglu et al. Antigen arrays for profiling autoantibody repertoires
Zhang et al. Identification of DNA–protein binding sites by bootstrap multiple convolutional neural networks on sequence information
Wu et al. Detecting overlapping protein complexes by rough-fuzzy clustering in protein-protein interaction networks
Barrows et al. Biolayer interferometry for DNA-protein interactions
Ji et al. DeepCDpred: Inter-residue distance and contact prediction for improved prediction of protein structure
Ali et al. Comparison of large networks with sub-sampling strategies
Altenburg et al. Ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of phosphorylated and cross-linked peptides
Lanchantin et al. Transfer learning for predicting virus-host protein interactions for novel virus sequences
Bourquard et al. A collaborative filtering approach for protein-protein docking scoring functions
Pan et al. Machine and deep learning for prediction of subcellular localization
CN115171811A (zh) 一种基于胶囊动态注意力机制的药物虚拟筛选方法
Koo et al. Interpreting deep neural networks beyond attribution methods: quantifying global importance of genomic features
Silva et al. Improving protein interaction prediction in GenPPi: a novel interaction sampling approach preserving network topology
Sun et al. BPDA2d—a 2D global optimization-based Bayesian peptide detection algorithm for liquid chromatograph–mass spectrometry
Sanchez-Gomez et al. A supervised multiclass framework for mineral classification of Iberian beads
Qin et al. Mapping cell structure across scales by fusing protein images and interactions
Senel et al. Optocoder: computational decoding of spatially indexed bead arrays

Legal Events

Date Code Title Description
EEER Examination request

Effective date: 20200824

MPN Maintenance fee for patent paid

Free format text: FEE DESCRIPTION TEXT: MF (PATENT, 6TH ANNIV.) - STANDARD

Year of fee payment: 6

U00 Fee paid

Free format text: ST27 STATUS EVENT CODE: A-4-4-U10-U00-U101 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE REQUEST RECEIVED

Effective date: 20241230

U11 Full renewal or maintenance fee paid

Free format text: ST27 STATUS EVENT CODE: A-4-4-U10-U11-U102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE PAYMENT DETERMINED COMPLIANT

Effective date: 20241230

Free format text: ST27 STATUS EVENT CODE: A-4-4-U10-U11-U102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE PAYMENT PAID IN FULL

Effective date: 20241230

MPN Maintenance fee for patent paid

Free format text: FEE DESCRIPTION TEXT: MF (PATENT, 7TH ANNIV.) - STANDARD

Year of fee payment: 7

U00 Fee paid

Free format text: ST27 STATUS EVENT CODE: A-4-4-U10-U00-U101 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE REQUEST RECEIVED

Effective date: 20260218

U11 Full renewal or maintenance fee paid

Free format text: ST27 STATUS EVENT CODE: A-4-4-U10-U11-U102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE PAYMENT PAID IN FULL

Effective date: 20260218