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WO2007098130A3 - Novel pooling and deconvolution strategy for large scale screening - Google Patents

Novel pooling and deconvolution strategy for large scale screening Download PDF

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Publication number
WO2007098130A3
WO2007098130A3 PCT/US2007/004313 US2007004313W WO2007098130A3 WO 2007098130 A3 WO2007098130 A3 WO 2007098130A3 US 2007004313 W US2007004313 W US 2007004313W WO 2007098130 A3 WO2007098130 A3 WO 2007098130A3
Authority
WO
WIPO (PCT)
Prior art keywords
deconvolution
pooling
novel
proteins
strategy
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/US2007/004313
Other languages
French (fr)
Other versions
WO2007098130A9 (en
WO2007098130A2 (en
Inventor
Jing Huang
Fulai Jin
Tony R Hazbun
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.)
Purdue Research Foundation
University of California Berkeley
University of California San Diego UCSD
Original Assignee
Purdue Research Foundation
University of California Berkeley
University of California San Diego UCSD
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 Purdue Research Foundation, University of California Berkeley, University of California San Diego UCSD filed Critical Purdue Research Foundation
Publication of WO2007098130A2 publication Critical patent/WO2007098130A2/en
Publication of WO2007098130A9 publication Critical patent/WO2007098130A9/en
Anticipated expiration legal-status Critical
Publication of WO2007098130A3 publication Critical patent/WO2007098130A3/en
Ceased legal-status Critical Current

Links

Classifications

    • 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
    • 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
    • G16C20/64—Screening of libraries

Landscapes

  • Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Library & Information Science (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Physics & Mathematics (AREA)
  • Theoretical Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Evolutionary Biology (AREA)
  • Biotechnology (AREA)
  • Biochemistry (AREA)
  • Molecular Biology (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biophysics (AREA)
  • Medicinal Chemistry (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Computing Systems (AREA)
  • Investigating Or Analysing Biological Materials (AREA)

Abstract

Embodiments of the present invention provide methods, systems, kits, and apparatus for data analysis to detect interactions between atoms, molecules and/or cells. One embodiment of the present invention provides for a novel pooling-deconvolution strategy that can dramatically decrease the effort required to generate large-scale data sets. This 'PI-Deconvolution' strategy employs an N-digit base-X imaginary coding of XN probe proteins (baits or preys) and allows the screening of the baits in X*N pools, with N replicates for each bait. Deconvolution of proteins with their binding partners can be achieved by reading the prey's profile from the X*N experiments. The method can be used to screen XN bait or prey proteins.
PCT/US2007/004313 2006-02-16 2007-02-16 Novel pooling and deconvolution strategy for large scale screening Ceased WO2007098130A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US77431706P 2006-02-16 2006-02-16
US60/774,317 2006-02-16

Publications (3)

Publication Number Publication Date
WO2007098130A2 WO2007098130A2 (en) 2007-08-30
WO2007098130A9 WO2007098130A9 (en) 2007-10-18
WO2007098130A3 true WO2007098130A3 (en) 2008-11-06

Family

ID=38437936

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2007/004313 Ceased WO2007098130A2 (en) 2006-02-16 2007-02-16 Novel pooling and deconvolution strategy for large scale screening

Country Status (1)

Country Link
WO (1) WO2007098130A2 (en)

Families Citing this family (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10208347B2 (en) * 2016-05-25 2019-02-19 Bioinventors & Entrepreneurs Network, Llc Attribute sieving and profiling with sample enrichment by optimized pooling

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030032066A1 (en) * 2001-03-19 2003-02-13 Pierre Legrain Protein-protein interaction map inference using interacting domain profile pairs
US20030165873A1 (en) * 2001-03-02 2003-09-04 Come Jon H. Three hybrid assay system

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030165873A1 (en) * 2001-03-02 2003-09-04 Come Jon H. Three hybrid assay system
US20030032066A1 (en) * 2001-03-19 2003-02-13 Pierre Legrain Protein-protein interaction map inference using interacting domain profile pairs

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
ITO ET AL.: "Toward a protein-protein interaction map of the building yeast: A comprehensive system to examine two-hybrid interactions in all possible combination between the yeast proteins", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 97, no. 3, 1 February 2000 (2000-02-01), pages 1143 - 1147 *
TAVERNIER ET AL.: "MAPPIT: a cytokine receptor-based two-hybrid method in mammalian cells", CLINICAL & EXPERIMENTAL ALLERGY, vol. 32, 2002, pages 1397 - 1404, XP055045545 *

Also Published As

Publication number Publication date
WO2007098130A9 (en) 2007-10-18
WO2007098130A2 (en) 2007-08-30

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