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WO2003088004A3 - The cop protein design tool - Google Patents

The cop protein design tool Download PDF

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Publication number
WO2003088004A3
WO2003088004A3 PCT/US2003/011613 US0311613W WO03088004A3 WO 2003088004 A3 WO2003088004 A3 WO 2003088004A3 US 0311613 W US0311613 W US 0311613W WO 03088004 A3 WO03088004 A3 WO 03088004A3
Authority
WO
WIPO (PCT)
Prior art keywords
ligands
design tool
protein design
cop protein
list
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.)
Ceased
Application number
PCT/US2003/011613
Other languages
French (fr)
Other versions
WO2003088004A2 (en
Inventor
William A Goddard
Nagarajan Vaidehi
Deqiang Zhang
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.)
California Institute of Technology
Original Assignee
California Institute of Technology
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 California Institute of Technology filed Critical California Institute of Technology
Priority to EP03718406A priority Critical patent/EP1573441A2/en
Priority to AU2003221944A priority patent/AU2003221944A1/en
Publication of WO2003088004A2 publication Critical patent/WO2003088004A2/en
Anticipated expiration legal-status Critical
Publication of WO2003088004A3 publication Critical patent/WO2003088004A3/en
Ceased legal-status Critical Current

Links

Classifications

    • 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
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/93—Ligases (6)
    • 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
    • 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
    • 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
    • G16B20/30—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
    • 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
    • G16B15/00—ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Chemical & Material Sciences (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Medical Informatics (AREA)
  • Biophysics (AREA)
  • Molecular Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Organic Chemistry (AREA)
  • Medicinal Chemistry (AREA)
  • Biomedical Technology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Peptides Or Proteins (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)

Abstract

The instant invention provides methods and implementing computer software for designing mutant proteins (or 'Target Protein or TP') that will preferentially bind one list of prespecified ligands (Active Ligands or AL) with respect to another list of ligands (The Inactive Ligands or IL).
PCT/US2003/011613 2002-04-12 2003-04-14 The cop protein design tool Ceased WO2003088004A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
EP03718406A EP1573441A2 (en) 2002-04-12 2003-04-14 The cop protein design tool
AU2003221944A AU2003221944A1 (en) 2002-04-12 2003-04-14 The cop protein design tool

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US37207402P 2002-04-12 2002-04-12
US60/372,074 2002-04-12

Publications (2)

Publication Number Publication Date
WO2003088004A2 WO2003088004A2 (en) 2003-10-23
WO2003088004A3 true WO2003088004A3 (en) 2007-07-26

Family

ID=29250787

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2003/011613 Ceased WO2003088004A2 (en) 2002-04-12 2003-04-14 The cop protein design tool

Country Status (3)

Country Link
EP (1) EP1573441A2 (en)
AU (1) AU2003221944A1 (en)
WO (1) WO2003088004A2 (en)

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7139665B2 (en) * 2002-02-27 2006-11-21 California Institute Of Technology Computational method for designing enzymes for incorporation of non natural amino acids into proteins

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7139665B2 (en) * 2002-02-27 2006-11-21 California Institute Of Technology Computational method for designing enzymes for incorporation of non natural amino acids into proteins

Non-Patent Citations (6)

* Cited by examiner, † Cited by third party
Title
BRICK P. ET AL.: "Structure of tyrosyl-tRNA synthetase refined at 2.3 A resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate", J. MOL. BIOL., vol. 208, no. 1, 5 July 1989 (1989-07-05), pages 83 - 98, XP002950541 *
KOWAL A.K. ET AL.: "Twenty-first aminoacyl-tRNA synthetase-suppressor tRNA pairs for possible use in site-specific incorporation of amino acid analogues into proteins in eukaryotes and in eubacteria", PNAS, vol. 98, no. 5, 27 February 2001 (2001-02-27), pages 2268 - 2273, XP002974767 *
LENGAUER T. ET AL.: "Computational methods for biomolecular docking", CURRENT OPINION IN STRUCTURAL BIOLOGY, vol. 6, 1996, pages 402 - 406, XP003015662 *
OHNO S. ET AL.: "Changing the amino acid specificity of yeast tyrosyl-tRNA synthetase by genetic engineering", J. BIOCHEM., vol. 130, no. 3, September 2001 (2001-09-01), pages 417 - 423, XP002950536 *
ROULD M.A. ET AL.: "Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase", NATURE, vol. 352, 1991, pages 213 - 218, XP003015663 *
ZHANG D. ET AL.: "Structure-based design of mutant Methanococcus jannaschii tyrosyl-tRNA synthetase for incorporation of O-methyl-L-tyrosine", PNAS, vol. 99, no. 10, 14 May 2002 (2002-05-14), pages 6579 - 6584, XP002976470 *

Also Published As

Publication number Publication date
AU2003221944A8 (en) 2003-10-27
WO2003088004A2 (en) 2003-10-23
EP1573441A2 (en) 2005-09-14
AU2003221944A1 (en) 2003-10-27

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