EP1514216A4 - Generation and selection of protein library in silico - Google Patents

Generation and selection of protein library in silico

Info

Publication number
EP1514216A4
EP1514216A4 EP03755415A EP03755415A EP1514216A4 EP 1514216 A4 EP1514216 A4 EP 1514216A4 EP 03755415 A EP03755415 A EP 03755415A EP 03755415 A EP03755415 A EP 03755415A EP 1514216 A4 EP1514216 A4 EP 1514216A4
Authority
EP
European Patent Office
Prior art keywords
silico
selection
generation
protein library
library
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.)
Withdrawn
Application number
EP03755415A
Other languages
German (de)
French (fr)
Other versions
EP1514216A2 (en
Inventor
Peizhi Luo
Mark Hsieh
Pingyu Zhong
Caili Wang
Yicheng Cao
Shengjiang Liu
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.)
Abmaxis Inc
Original Assignee
Abmaxis 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
Priority claimed from US10/153,159 external-priority patent/US7117096B2/en
Priority claimed from US10/153,176 external-priority patent/US20030022240A1/en
Application filed by Abmaxis Inc filed Critical Abmaxis Inc
Publication of EP1514216A2 publication Critical patent/EP1514216A2/en
Publication of EP1514216A4 publication Critical patent/EP1514216A4/en
Withdrawn legal-status Critical Current

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/22—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against growth factors ; against growth regulators
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • 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
    • 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
    • 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
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
    • C07K2317/24—Immunoglobulins specific features characterized by taxonomic origin containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/60—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments
    • C07K2317/62—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments comprising only variable region components
    • C07K2317/622—Single chain antibody (scFv)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • 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
    • G16B20/50—Mutagenesis

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Molecular Biology (AREA)
  • Analytical Chemistry (AREA)
  • Library & Information Science (AREA)
  • Biochemistry (AREA)
  • Genetics & Genomics (AREA)
  • Organic Chemistry (AREA)
  • Medicinal Chemistry (AREA)
  • Immunology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Computing Systems (AREA)
  • Peptides Or Proteins (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
EP03755415A 2002-05-20 2003-05-20 Generation and selection of protein library in silico Withdrawn EP1514216A4 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US153159 1988-02-08
US153176 1993-11-16
US10/153,159 US7117096B2 (en) 2001-04-17 2002-05-20 Structure-based selection and affinity maturation of antibody library
US10/153,176 US20030022240A1 (en) 2001-04-17 2002-05-20 Generation and affinity maturation of antibody library in silico
PCT/US2003/016037 WO2003099999A2 (en) 2002-05-20 2003-05-20 Generation and selection of protein library in silico

Publications (2)

Publication Number Publication Date
EP1514216A2 EP1514216A2 (en) 2005-03-16
EP1514216A4 true EP1514216A4 (en) 2010-01-06

Family

ID=29586304

Family Applications (1)

Application Number Title Priority Date Filing Date
EP03755415A Withdrawn EP1514216A4 (en) 2002-05-20 2003-05-20 Generation and selection of protein library in silico

Country Status (7)

Country Link
EP (1) EP1514216A4 (en)
JP (1) JP2005526518A (en)
CN (1) CN1672160B (en)
AU (1) AU2003248548B2 (en)
CA (1) CA2485732A1 (en)
SG (1) SG135053A1 (en)
WO (1) WO2003099999A2 (en)

Families Citing this family (41)

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US7667004B2 (en) * 2001-04-17 2010-02-23 Abmaxis, Inc. Humanized antibodies against vascular endothelial growth factor
AU2004202566B2 (en) * 2004-06-11 2011-07-21 Li-Te Chin Method for Producing Human Antibodies with Properties of Agonist, Antagonist, or Inverse Agonist
CZ200755A3 (en) 2004-07-26 2007-04-11 Biogen Idec Ma Inc. Anti-CD154 antibody peptides
DK2343380T3 (en) 2004-11-16 2019-09-09 Humanigen Inc IMMUNOGLOBULIN VARIABLE REGION CARTRIDGE REPLACEMENT
CA2600929A1 (en) 2005-03-04 2006-09-14 Biogen Idec Ma Inc. Methods of humanizing immunoglobulin variable regions through rational modification of complementarity determining residues
WO2007109254A2 (en) * 2006-03-17 2007-09-27 Biogen Idec Ma Inc. Stabilized polypeptide compositions
CA2664681C (en) 2006-10-02 2020-07-07 Sea Lane Biotechnologies, Llc Design and construction of diverse synthetic peptide and polypeptide libraries
WO2008094547A2 (en) * 2007-01-31 2008-08-07 Jiaan Yang Methods, systems, algorithyms and means for describing the possible conformations of actual and theoretical proteins and for evaluating actual and theoretical proteins with respect to folding, overall shape and structural motifs
CA2742968C (en) 2008-11-07 2020-06-09 Fabrus Llc Combinatorial antibody libraries and uses thereof
US9079953B2 (en) * 2009-06-17 2015-07-14 Abbvie Biotherapeutics Inc. Anti-VEGF antibodies and their uses
WO2011047146A2 (en) * 2009-10-14 2011-04-21 Centocor Ortho Biotech Inc. Methods of affinity maturing antibodies
JPWO2013171810A1 (en) 2012-05-14 2016-01-07 パナソニックＩｐマネジメント株式会社 Method for obtaining thermostable antibody-displayed phage
US20140154255A1 (en) 2012-11-30 2014-06-05 Abbvie Biotherapeutics Inc. Anti-vegf antibodies and their uses
BR112015018454B1 (en) * 2013-01-31 2023-05-09 Codexis, Inc METHOD OF IDENTIFICATION OF AMINO ACIDS, NUCLEOTIDES, POLYPEPTIDES, OR POLYNUCLEOTIDES, AND, COMPUTER SYSTEM
CN104805507B (en) * 2014-01-29 2019-01-22 杭州康万达医药科技有限公司 phage display library and its application and preparation method
US10665324B2 (en) 2014-07-07 2020-05-26 Yeda Research And Development Co. Ltd. Method of computational protein design
GB201500464D0 (en) * 2015-01-12 2015-02-25 Crescendo Biolog Ltd Method of producing optimised therapeutic molecules
US10336816B2 (en) * 2015-02-24 2019-07-02 Academia Sinica Phage-displayed single-chain variable fragment library
CN104789555A (en) * 2015-04-29 2015-07-22 江南大学 Method of expressing regulatory element based on evolution gene by synthesizing single-chain DNA library
JP6558754B2 (en) 2015-08-07 2019-08-14 富士通株式会社 Information processing apparatus, index dimension extraction method, and index dimension extraction program
PE20181363A1 (en) 2015-09-23 2018-08-27 Genentech Inc OPTIMIZED VARIANTS OF ANTI-VEGF ANTIBODIES
CN106290908A (en) * 2016-08-07 2017-01-04 查文娟 A kind of for kidney injury detection test kit
US20190214108A1 (en) * 2016-09-16 2019-07-11 Osaka University Immunological entity clustering software
CN106905435B (en) * 2017-03-13 2020-04-10 武汉海沙百得生物技术有限公司 Method for preparing binding protein based on protein A mutant
CN110730822B (en) * 2017-04-18 2024-03-08 X-化学有限公司 Methods for identifying compounds
EP3669018A4 (en) 2017-08-18 2021-05-26 Nautilus Biotechnology, Inc. Methods of selecting binding reagents
AU2018367622B2 (en) * 2017-11-20 2022-12-22 Nantbio, Inc. mRNA display antibody library and methods
CN108304691B (en) * 2018-02-09 2021-05-18 北京矿冶科技集团有限公司 Fragment-based flotation agent molecule design method
CN108491692B (en) * 2018-03-09 2023-07-21 中国科学院生态环境研究中心 Method for constructing antibiotic resistance gene database
CN108763870B (en) * 2018-05-09 2021-08-03 浙江工业大学 Construction method of multi-domain protein Linker
CN109002690B (en) * 2018-06-08 2021-05-18 济南大学 Method for predicting side chain structure of mutant amino acid by constructing CHARMM ROTAMERS force field
CN108959846B (en) * 2018-07-03 2021-09-14 南昌立德生物技术有限公司 Affinity free energy decomposition algorithm for computer-aided pilot medicament optimization design
CN109243526B (en) * 2018-07-12 2021-08-03 浙江工业大学 Protein structure prediction method based on specific fragment crossing
CN109086568B (en) * 2018-08-16 2022-03-11 福建工程学院 Computer antibody combined mutation evolution system and method and information data processing terminal
CN109801679B (en) * 2019-01-15 2021-02-02 广州柿宝生物科技有限公司 Mathematical sequence reconstruction method for long-chain molecules
WO2020208555A1 (en) * 2019-04-09 2020-10-15 Eth Zurich Systems and methods to classify antibodies
EP3982369A4 (en) 2019-06-07 2023-06-14 Chugai Seiyaku Kabushiki Kaisha Information processing system, information processing method, program, and method for producing antigen-binding molecule or protein
CN115349128A (en) * 2020-02-13 2022-11-15 齐默尔根公司 Metagenomic libraries and natural product discovery platform
CN111370074B (en) * 2020-02-27 2023-07-07 北京晶泰科技有限公司 Method and device for generating molecular sequence and computing equipment
CN111462815B (en) * 2020-03-27 2023-05-02 上海祥耀生物科技有限责任公司 Construction method and device of antibody library
CN112102883B (en) * 2020-08-20 2023-12-08 深圳华大生命科学研究院 Base sequence coding method and system in FASTQ file compression

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002084277A1 (en) * 2001-04-17 2002-10-24 Abmaxis, Inc. Structure-based construction of human antibody library

Family Cites Families (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU3415395A (en) * 1994-08-26 1996-03-22 Eli Lilly And Company Antibody constructs with cdr switched variable regions

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002084277A1 (en) * 2001-04-17 2002-10-24 Abmaxis, Inc. Structure-based construction of human antibody library

Also Published As

Publication number Publication date
WO2003099999A3 (en) 2004-09-16
JP2005526518A (en) 2005-09-08
AU2003248548B2 (en) 2010-03-11
CA2485732A1 (en) 2003-12-04
CN1672160B (en) 2010-06-09
CN1672160A (en) 2005-09-21
WO2003099999A2 (en) 2003-12-04
EP1514216A2 (en) 2005-03-16
SG135053A1 (en) 2007-09-28
AU2003248548A1 (en) 2003-12-12

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Inventor name: LIU, SHENGJIANG

Inventor name: CAO, YICHENG

Inventor name: WANG, CAILI

Inventor name: ZHONG, PINGYU

Inventor name: HSIEH, MARKMERCK & CO, INC

Inventor name: LUO, PEIZHIMERCK & CO, INC

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