WO2004027540A3 - A computational method for predicting intramolecular and intermolecular biopolymer interactions - Google Patents

A computational method for predicting intramolecular and intermolecular biopolymer interactions Download PDF

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Publication number
WO2004027540A3
WO2004027540A3 PCT/US2002/030656 US0230656W WO2004027540A3 WO 2004027540 A3 WO2004027540 A3 WO 2004027540A3 US 0230656 W US0230656 W US 0230656W WO 2004027540 A3 WO2004027540 A3 WO 2004027540A3
Authority
WO
WIPO (PCT)
Prior art keywords
intramolecular
intermolecular
interactions
predicting
biopolymers
Prior art date
Application number
PCT/US2002/030656
Other languages
French (fr)
Other versions
WO2004027540A2 (en
Inventor
Phillip S Pang
Eckhard Jankowsky
Anna Marie Pyle
Original Assignee
Univ Columbia
Phillip S Pang
Eckhard Jankowsky
Anna Marie Pyle
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 Univ Columbia, Phillip S Pang, Eckhard Jankowsky, Anna Marie Pyle filed Critical Univ Columbia
Priority to AU2002334688A priority Critical patent/AU2002334688A1/en
Priority to CA002499412A priority patent/CA2499412A1/en
Priority to PCT/US2002/030656 priority patent/WO2004027540A2/en
Publication of WO2004027540A2 publication Critical patent/WO2004027540A2/en
Publication of WO2004027540A3 publication Critical patent/WO2004027540A3/en

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Classifications

    • 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
    • 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
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • 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

Abstract

Disclosed is a computational method for predicting intramolecular and intermolecular biopolymer interactions which provides an improved way of determining structure and function information, including intramolecular and intermolecular interactions using an ab initio-type approach, i.e. using only sequence information. The method is a widely applicable sequence-mining tool capable of detecting both intramolecular and intermolecular interactions for all biopolymers, including, but not limited to, DNA, RNA and protein. It possesses an adaptive screening process that allows for high accuracy. It can be an entirely rule-free, unbiased methodology, and thus can detect novel interactions for all biopolymers. Due to the incorporation of a misalignment process, it can be used iteratively and is capable of refining its own predictions and detecting and managing errors. Therefore, the disclosed method also provides a technique for more accurately determining (and refining) sequence alignments.
PCT/US2002/030656 2002-09-23 2002-09-23 A computational method for predicting intramolecular and intermolecular biopolymer interactions WO2004027540A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
AU2002334688A AU2002334688A1 (en) 2002-09-23 2002-09-23 A computational method for predicting intramolecular and intermolecular biopolymer interactions
CA002499412A CA2499412A1 (en) 2002-09-23 2002-09-23 A computational method for predicting intramolecular and intermolecular biopolymer interactions
PCT/US2002/030656 WO2004027540A2 (en) 2002-09-23 2002-09-23 A computational method for predicting intramolecular and intermolecular biopolymer interactions

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
PCT/US2002/030656 WO2004027540A2 (en) 2002-09-23 2002-09-23 A computational method for predicting intramolecular and intermolecular biopolymer interactions

Publications (2)

Publication Number Publication Date
WO2004027540A2 WO2004027540A2 (en) 2004-04-01
WO2004027540A3 true WO2004027540A3 (en) 2005-03-24

Family

ID=32028467

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2002/030656 WO2004027540A2 (en) 2002-09-23 2002-09-23 A computational method for predicting intramolecular and intermolecular biopolymer interactions

Country Status (3)

Country Link
AU (1) AU2002334688A1 (en)
CA (1) CA2499412A1 (en)
WO (1) WO2004027540A2 (en)

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5436850A (en) * 1991-07-11 1995-07-25 The Regents Of The University Of California Method to identify protein sequences that fold into a known three-dimensional structure
US5557535A (en) * 1993-04-28 1996-09-17 Immunex Corporation Method and system for protein modeling
US5878373A (en) * 1996-12-06 1999-03-02 Regents Of The University Of California System and method for determining three-dimensional structure of protein sequences

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5436850A (en) * 1991-07-11 1995-07-25 The Regents Of The University Of California Method to identify protein sequences that fold into a known three-dimensional structure
US5557535A (en) * 1993-04-28 1996-09-17 Immunex Corporation Method and system for protein modeling
US5878373A (en) * 1996-12-06 1999-03-02 Regents Of The University Of California System and method for determining three-dimensional structure of protein sequences

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
BAKER, D.: "A surprising simplicity to protein folding", NATURE, vol. 405, 4 May 2000 (2000-05-04), pages 39 - 42, XP002974894 *
SANCHEZ, R. ET AL.: "Protein structure modeling for structural genomics", NATURE STRUCTURAL BIOLOGY SUPPLEMENT, November 2000 (2000-11-01), pages 986 - 990, XP002974893 *

Also Published As

Publication number Publication date
AU2002334688A8 (en) 2004-04-08
WO2004027540A2 (en) 2004-04-01
AU2002334688A1 (en) 2004-04-08
CA2499412A1 (en) 2004-04-01

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WO2004027540A3 (en) A computational method for predicting intramolecular and intermolecular biopolymer interactions

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