IT201900009531A1 - Metodo per l’ottimizzazione delle proprietà fisico-chimiche delle sequenze biologiche implementabile via computer - Google Patents

Metodo per l’ottimizzazione delle proprietà fisico-chimiche delle sequenze biologiche implementabile via computer

Info

Publication number
IT201900009531A1
IT201900009531A1 IT102019000009531A IT201900009531A IT201900009531A1 IT 201900009531 A1 IT201900009531 A1 IT 201900009531A1 IT 102019000009531 A IT102019000009531 A IT 102019000009531A IT 201900009531 A IT201900009531 A IT 201900009531A IT 201900009531 A1 IT201900009531 A1 IT 201900009531A1
Authority
IT
Italy
Prior art keywords
optimizing
physical
chemical properties
via computer
biological sequences
Prior art date
Application number
IT102019000009531A
Other languages
English (en)
Inventor
Guido Uguzzoni
Andrea Pagnani
Cossío Díaz Jorge Fernández De
Original Assignee
Torino Politecnico
Ct Inmunologia Molecular
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 Torino Politecnico, Ct Inmunologia Molecular filed Critical Torino Politecnico
Priority to IT102019000009531A priority Critical patent/IT201900009531A1/it
Priority to US17/620,768 priority patent/US20220344006A1/en
Priority to JP2021567991A priority patent/JP2022538378A/ja
Priority to CA3141526A priority patent/CA3141526A1/en
Priority to PCT/IB2020/055780 priority patent/WO2020255058A1/en
Priority to CN202080044735.8A priority patent/CN114008711A/zh
Priority to EP20743310.3A priority patent/EP3994695A1/en
Publication of IT201900009531A1 publication Critical patent/IT201900009531A1/it
Priority to IL289091A priority patent/IL289091A/en

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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/50—Mutagenesis
    • 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
    • G16B35/00—ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
    • G16B35/20—Screening of libraries
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/10—Complex mathematical operations
    • G06F17/11—Complex mathematical operations for solving equations, e.g. nonlinear equations, general mathematical optimization problems
    • 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
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

Landscapes

  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Theoretical Computer Science (AREA)
  • Molecular Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Genetics & Genomics (AREA)
  • Chemical & Material Sciences (AREA)
  • Mathematical Physics (AREA)
  • General Physics & Mathematics (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Mathematical Analysis (AREA)
  • Computational Mathematics (AREA)
  • Library & Information Science (AREA)
  • Pure & Applied Mathematics (AREA)
  • Mathematical Optimization (AREA)
  • Data Mining & Analysis (AREA)
  • Algebra (AREA)
  • Software Systems (AREA)
  • General Engineering & Computer Science (AREA)
  • Databases & Information Systems (AREA)
  • Operations Research (AREA)
  • Biochemistry (AREA)
  • Physiology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
IT102019000009531A 2019-06-19 2019-06-19 Metodo per l’ottimizzazione delle proprietà fisico-chimiche delle sequenze biologiche implementabile via computer IT201900009531A1 (it)

Priority Applications (8)

Application Number Priority Date Filing Date Title
IT102019000009531A IT201900009531A1 (it) 2019-06-19 2019-06-19 Metodo per l’ottimizzazione delle proprietà fisico-chimiche delle sequenze biologiche implementabile via computer
US17/620,768 US20220344006A1 (en) 2019-06-19 2020-06-19 Computer implemented method to optimize physical-chemical properties of biological sequences
JP2021567991A JP2022538378A (ja) 2019-06-19 2020-06-19 生物学的シーケンスの物理的／化学的特性を最適化するコンピュータ実施方法
CA3141526A CA3141526A1 (en) 2019-06-19 2020-06-19 Computer implemented method to optimize physical-chemical properties of biological sequences
PCT/IB2020/055780 WO2020255058A1 (en) 2019-06-19 2020-06-19 Computer implemented method to optimize physical-chemical properties of biological sequences
CN202080044735.8A CN114008711A (zh) 2019-06-19 2020-06-19 优化生物序列理化性质的由计算机实现的方法
EP20743310.3A EP3994695A1 (en) 2019-06-19 2020-06-19 Computer implemented method to optimize physical-chemical properties of biological sequences
IL289091A IL289091A (en) 2019-06-19 2021-12-16 A computer-implemented method for optimizing physical-chemical properties of biological sequences

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
IT102019000009531A IT201900009531A1 (it) 2019-06-19 2019-06-19 Metodo per l’ottimizzazione delle proprietà fisico-chimiche delle sequenze biologiche implementabile via computer

Publications (1)

Publication Number Publication Date
IT201900009531A1 true IT201900009531A1 (it) 2020-12-19

Family

ID=68582097

Family Applications (1)

Application Number Title Priority Date Filing Date
IT102019000009531A IT201900009531A1 (it) 2019-06-19 2019-06-19 Metodo per l’ottimizzazione delle proprietà fisico-chimiche delle sequenze biologiche implementabile via computer

Country Status (8)

Country Link
US (1) US20220344006A1 (it)
EP (1) EP3994695A1 (it)
JP (1) JP2022538378A (it)
CN (1) CN114008711A (it)
CA (1) CA3141526A1 (it)
IL (1) IL289091A (it)
IT (1) IT201900009531A1 (it)
WO (1) WO2020255058A1 (it)

Families Citing this family (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN113886252B (zh) * 2021-09-30 2023-05-23 四川大学 基于热力图的回归测试用例优先级确定方法
EP4227951A1 (en) * 2022-02-11 2023-08-16 Samsung Display Co., Ltd. Method for predicting and optimizing properties of a molecule

Family Cites Families (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20020169730A1 (en) * 2001-08-29 2002-11-14 Emmanuel Lazaridis Methods for classifying objects and identifying latent classes
ES2774965T3 (es) * 2013-09-27 2020-07-23 Codexis Inc Modelado predictivo a base de estructura

Non-Patent Citations (19)

* Cited by examiner, † Cited by third party
Title
ALAN F. RUBIN ET AL., GENOME BIOLOGY, 2017
B. SHEN ET AL: "Physicochemical feature-based classification of amino acid mutations", PROTEIN ENGINEERING, DESIGN AND SELECTION, vol. 21, no. 1, 19 December 2007 (2007-12-19), GB, pages 37 - 44, XP055677810, ISSN: 1741-0126, DOI: 10.1093/protein/gzm084 *
BARRAT-CHARLAIX ET AL., SCIENTIFIC REPORTS
C. L. ARAYA ET AL.: "A fundamental property, ''protein thermodynamic stability, revealed flux from large-scale measurements of protein function", PNAS, 2012
C. OLSON ET AL.: "A comprehensive biophysical description of pairwise epistasis throughout an authorities re protein domain", CURRENT BIOLOGY, 2014
D. M. FOWLER ET AL.: "High-resolution mapping of protein sequence-function relationships", NATURE METHODS, 2010
FOWLER D. M.FIELDS S., NAT METHODS, 2014
FOWLER, DOUGLAS M.STANLEY FIELDS: "Deep mutational scanning: a new style of protein science", NATURE METHODS, vol. 11.8, 2014, pages 801
HOPF ET AL., NATURE BIOTECHNOLOGY
JESSE D BLOOM, BMC BIOINFORMATICS, 2015
M. M GROMIHA ET AL: "ProTherm, Thermodynamic Database for Proteins and Mutants: developments in version 3.0", NUCLEIC ACIDS RESEARCH, 1 January 2002 (2002-01-01), pages 301 - 302, XP055677881, Retrieved from the Internet <URL:https://academic.oup.com/nar/article-pdf/27/1/286/4065360/27-1-286.pdf> [retrieved on 20200319], DOI: 10.1093/nar/30.1.301 *
OTWINOWSKI, JAKUB: "Biophysical inference of epistasis and the effects of mutations on protein stability and function", MOLECULAR BIOLOGY AND EVOLUTION, vol. 35.10, 2018, pages 2345 - 2354
PACKERLIU, NATURE REVIEWS GENETICS, 2015
PO-SSU HUANG ET AL., NATURE, 2016
RAZA WASEEM ET AL: "Optimization and characterization of a polysaccharide produced byPseudomonas fluorescensWR-1 and its antioxidant activity", CARBOHYDRATE POLYMERS, vol. 90, no. 2, 1 October 2012 (2012-10-01), pages 921 - 929, XP028931965, ISSN: 0144-8617, DOI: 10.1016/J.CARBPOL.2012.06.021 *
TABARESTANI H S ET AL: "Optimization of physico-chemical properties of gelatin extracted from fish skin of rainbow trout (Onchorhynchusmykiss)", BIORESOURCE TECHNOLOGY, ELSEVIER, AMSTERDAM, NL, vol. 101, no. 15, 1 August 2010 (2010-08-01), pages 6207 - 6214, XP027018570, ISSN: 0960-8524, [retrieved on 20100421] *
Z. WU ET AL.: "machine learning-assisted directed protein evolution with combinatorial! Libraries", ARXIV PREPRINT
ZHUO Z ET AL.: "Recent Advances in technology and aptamer SELEX Applications in Biomedicine", INT J MOL SKI., vol. 18, no. 10, 14 October 2017 (2017-10-14)
ZHUO Z ET AL.: "Recent Advances in technology and aptamer SELEX Applications", BIOMEDICINE INT J MOL SKI., vol. 18, no. 10, 14 October 2017 (2017-10-14)

Also Published As

Publication number Publication date
JP2022538378A (ja) 2022-09-02
CN114008711A (zh) 2022-02-01
US20220344006A1 (en) 2022-10-27
WO2020255058A1 (en) 2020-12-24
IL289091A (en) 2022-02-01
EP3994695A1 (en) 2022-05-11
CA3141526A1 (en) 2020-12-24

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