SG11201505977RA - Methods, systems, and software for identifying bio-molecules using models of multiplicative form - Google Patents

Methods, systems, and software for identifying bio-molecules using models of multiplicative form

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Publication number
SG11201505977RA
SG11201505977RA SG11201505977RA SG11201505977RA SG11201505977RA SG 11201505977R A SG11201505977R A SG 11201505977RA SG 11201505977R A SG11201505977R A SG 11201505977RA SG 11201505977R A SG11201505977R A SG 11201505977RA SG 11201505977R A SG11201505977R A SG 11201505977RA
Authority
SG
Singapore
Prior art keywords
models
molecules
software
systems
methods
Prior art date
Application number
SG11201505977RA
Inventor
Gregory Allan Cope
Nicholas John Agard
Original Assignee
Codexis 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 Codexis Inc filed Critical Codexis Inc
Publication of SG11201505977RA publication Critical patent/SG11201505977RA/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1058—Directional evolution of libraries, e.g. evolution of libraries is achieved by mutagenesis and screening or selection of mixed population of organisms
    • 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
    • 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
    • G16B10/00—ICT specially adapted for evolutionary bioinformatics, e.g. phylogenetic tree construction or analysis
    • 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 or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
    • 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
    • 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
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • 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
    • G16B35/00—ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
    • G16B35/10—Design of libraries
    • 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
    • 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
    • G16B5/20—Probabilistic models
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C10/00—Computational theoretical chemistry, i.e. ICT specially adapted for theoretical aspects of quantum chemistry, molecular mechanics, molecular dynamics or the like
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
    • G16C20/30—Prediction of properties of chemical compounds, compositions or mixtures
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
    • G16C20/50—Molecular design, e.g. of drugs
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
    • G16C20/60—In silico combinatorial chemistry
    • 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
SG11201505977RA 2013-01-31 2014-01-29 Methods, systems, and software for identifying bio-molecules using models of multiplicative form SG11201505977RA (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201361759276P 2013-01-31 2013-01-31
US201361799377P 2013-03-15 2013-03-15
PCT/US2014/013668 WO2014120821A1 (en) 2013-01-31 2014-01-29 Methods, systems, and software for identifying bio-molecules using models of multiplicative form

Publications (1)

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SG11201505977RA true SG11201505977RA (en) 2015-08-28

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SG11201505977RA SG11201505977RA (en) 2013-01-31 2014-01-29 Methods, systems, and software for identifying bio-molecules using models of multiplicative form

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US (4) US9684771B2 (en)
EP (2) EP2951579B1 (en)
JP (4) JP6377078B2 (en)
KR (3) KR20150113166A (en)
CN (3) CN109360608B (en)
AU (2) AU2014212432B2 (en)
BR (2) BR112015018454B1 (en)
CA (2) CA2899859C (en)
DK (1) DK2951754T3 (en)
IL (2) IL240055A0 (en)
LT (1) LT2951754T (en)
NZ (2) NZ710323A (en)
RU (2) RU2695146C2 (en)
SG (2) SG11201505969XA (en)
WO (2) WO2014120819A1 (en)

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AU2014212430B2 (en) 2019-06-20
JP2016504924A (en) 2016-02-18
EP2951579A4 (en) 2016-09-21
CA2899859A1 (en) 2014-08-07
RU2015136780A (en) 2017-03-10
RU2664695C2 (en) 2018-08-21
CN105074463A (en) 2015-11-18
IL240055A0 (en) 2015-09-24
EP2951754A1 (en) 2015-12-09
BR112015018449B1 (en) 2022-05-31
KR102215219B1 (en) 2021-02-16
BR112015018454A2 (en) 2018-12-04
AU2014212432A1 (en) 2015-08-06
AU2014212430A1 (en) 2015-08-06
KR102490720B1 (en) 2023-01-27
RU2695146C2 (en) 2019-07-22
KR20210005325A (en) 2021-01-13
AU2014212432B2 (en) 2019-09-19
CN105144190B (en) 2018-05-01
CN105144190A (en) 2015-12-09
NZ710299A (en) 2020-01-31
BR112015018449A2 (en) 2019-05-14
JP6433028B2 (en) 2018-12-05
JP6377078B2 (en) 2018-08-22
JP2016511884A (en) 2016-04-21
JP2018161148A (en) 2018-10-18
SG11201505969XA (en) 2015-08-28
JP6655670B2 (en) 2020-02-26
US20170204405A1 (en) 2017-07-20
LT2951754T (en) 2024-04-25
CN109360608A (en) 2019-02-19
KR20150113166A (en) 2015-10-07
CA2899859C (en) 2022-08-16
DK2951754T3 (en) 2024-04-15
JP2017189176A (en) 2017-10-19
US20140214391A1 (en) 2014-07-31
EP2951754A4 (en) 2016-11-30
WO2014120821A1 (en) 2014-08-07
IL240056A0 (en) 2015-09-24
US9684771B2 (en) 2017-06-20
BR112015018454B1 (en) 2023-05-09
EP2951579B1 (en) 2024-04-24
US9665694B2 (en) 2017-05-30
US20170211206A1 (en) 2017-07-27
CA2898777A1 (en) 2014-08-07
CN105074463B (en) 2018-09-25
CN109360608B (en) 2022-05-24
US20140221216A1 (en) 2014-08-07
RU2015136776A (en) 2017-03-10
EP2951579A1 (en) 2015-12-09
EP2951754B1 (en) 2024-03-20
KR20150113167A (en) 2015-10-07
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CA2898777C (en) 2024-01-02
WO2014120819A1 (en) 2014-08-07

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