SG135053A1 - Generation and selection of protein library in silico - Google Patents

Generation and selection of protein library in silico

Info

Publication number
SG135053A1
SG135053A1 SG200600435-2A SG2006004352A SG135053A1 SG 135053 A1 SG135053 A1 SG 135053A1 SG 2006004352 A SG2006004352 A SG 2006004352A SG 135053 A1 SG135053 A1 SG 135053A1
Authority
SG
Singapore
Prior art keywords
library
lead
sequence
protein
proteins
Prior art date
Application number
SG200600435-2A
Inventor
Peizhi Luo
Mark Hsieh
Pingyu Zhong
Caili Wang
Yicheng Cao
Shengjiang Liu
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 SG135053A1 publication Critical patent/SG135053A1/en

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)
  • Theoretical Computer Science (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Medical Informatics (AREA)
  • Biotechnology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Evolutionary Biology (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)
  • Computing Systems (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Peptides Or Proteins (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)

Abstract

The present invention provides a methodology for efficiently generating and screening protein libraries for optimized proteins with desirable biological functions, such as improved binding affinity towards biologically and/or therapeutically important target molecules. This process is carried out computationally in a high throughput manner by mining the ever-expanding databases of protein sequences of all organisms, especially human. In one embodiment, a method for constructing a library of designed proteins, comprising the steps of providing an amino acid sequence derived from a lead protein, the amino acid sequence being designated as a lead sequence; comparing the lead sequence with a plurality of tester protein sequences; and selecting from the plurality of tester protein sequences at least two peptide segments that have at least 15% sequence identity with the lead sequence, the selected peptide segments forming a hit library; and forming a library of designed proteins by substituting the lead sequence with the hit library. The library of designed proteins can be expressed in vitro or in vivo to produce a library of recombinant proteins that can be screened for novel or improved function(s) over the lead protein, such as an antibody against therapeutically important target. (no suitable figure)
SG200600435-2A 2002-05-20 2003-05-20 Generation and selection of protein library in silico SG135053A1 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
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

Publications (1)

Publication Number Publication Date
SG135053A1 true SG135053A1 (en) 2007-09-28

Family

ID=29586304

Family Applications (1)

Application Number Title Priority Date Filing Date
SG200600435-2A SG135053A1 (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)

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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
CN101072587B (en) 2004-07-26 2012-12-26 比奥根艾迪克Ma公司 Anti-cd154 antibodies
WO2006055778A2 (en) 2004-11-16 2006-05-26 Kalobios, Inc. Immunoglobulin variable region cassette exchange
EP1869084A2 (en) 2005-03-04 2007-12-26 Biogen Idec MA Inc. Methods of humanizing immunoglobulin variable regions through rational modification of complementarity determining residues
KR101516823B1 (en) * 2006-03-17 2015-05-07 바이오겐 아이덱 엠에이 인코포레이티드 Stabilized polypeptide compositions
AU2007303572A1 (en) 2006-10-02 2008-04-10 Sea Lane Biotechnologies, Llc Design and construction of diverse synthetic peptide and polypeptide libraries
JP2010517195A (en) * 2007-01-31 2010-05-20 桑迪▲亜▼医▲薬▼技▲術▼（上海）有限▲責▼任公司 Methods, systems, algorithms and means for the description of possible structures of actual and theoretical proteins, and for the evaluation of actual and theoretical proteins with respect to folding, overall shape and structure motifs
US9403904B2 (en) * 2008-11-07 2016-08-02 Fabrus, Inc. Anti-DLL4 antibodies and uses thereof
NZ596837A (en) * 2009-06-17 2014-02-28 Abbvie Biotherapeutics Inc Anti-vegf antibodies and their uses
DK2488867T3 (en) * 2009-10-14 2020-11-09 Janssen Biotech Inc PROCEDURES FOR AFFINITY MATURE OF 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
FI2951754T3 (en) * 2013-01-31 2024-05-16 Codexis Inc Methods, systems, and software for identifying bio-molecules with interacting components
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
ES2834849T3 (en) 2014-07-07 2021-06-18 Yeda Res & Dev Protein computational design method
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
MY191756A (en) * 2015-09-23 2022-07-14 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
JP6778932B2 (en) * 2016-09-16 2020-11-04 国立大学法人大阪大学 Immune 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
AU2018256367A1 (en) * 2017-04-18 2019-11-28 X-Chem, Inc. Methods for identifying compounds
WO2019036055A2 (en) 2017-08-18 2019-02-21 Ignite Biosciences, Inc. Methods of selecting binding reagents
KR102615744B1 (en) * 2017-11-20 2023-12-19 난트바이오 인코포레이티드 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
US20220157403A1 (en) * 2019-04-09 2022-05-19 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
IL294909A (en) * 2020-02-13 2022-09-01 Zymergen Inc Metagenomic library 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)

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Publication number Priority date Publication date Assignee Title
WO1996006625A1 (en) * 1994-08-26 1996-03-07 Eli Lilly And Company Antibody constructs with cdr switched variable regions

Family Cites Families (1)

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Publication number Priority date Publication date Assignee Title
US20030054407A1 (en) * 2001-04-17 2003-03-20 Peizhi Luo Structure-based construction of human antibody library

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1996006625A1 (en) * 1994-08-26 1996-03-07 Eli Lilly And Company Antibody constructs with cdr switched variable regions

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
FULLY SYNTHETIC HUMAN COMBINATORIAL ANTIBODY LIBRARIES (HUCAL) BASED ON MODULAR CONSENSUS FRAMEWORKS AND CDRS RANDOMISED WITH TRINUCLEOTID *

Also Published As

Publication number Publication date
AU2003248548A1 (en) 2003-12-12
AU2003248548B2 (en) 2010-03-11
WO2003099999A2 (en) 2003-12-04
CN1672160B (en) 2010-06-09
CA2485732A1 (en) 2003-12-04
CN1672160A (en) 2005-09-21
JP2005526518A (en) 2005-09-08
EP1514216A2 (en) 2005-03-16
WO2003099999A3 (en) 2004-09-16
EP1514216A4 (en) 2010-01-06

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