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WO2008134261A3 - A method for protein structure determination, gene identification, mutational analysis, and protein design - Google Patents

A method for protein structure determination, gene identification, mutational analysis, and protein design Download PDF

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Publication number
WO2008134261A3
WO2008134261A3 PCT/US2008/060786 US2008060786W WO2008134261A3 WO 2008134261 A3 WO2008134261 A3 WO 2008134261A3 US 2008060786 W US2008060786 W US 2008060786W WO 2008134261 A3 WO2008134261 A3 WO 2008134261A3
Authority
WO
WIPO (PCT)
Prior art keywords
protein
structure determination
mutational analysis
gene identification
design
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/US2008/060786
Other languages
French (fr)
Other versions
WO2008134261A2 (en
Inventor
Charles Michael Fortmann
Yeona Kang
David H. Coleman
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.)
Research Foundation of the State University of New York
Original Assignee
Research Foundation of the State University of New York
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 PCT/US2007/067639 external-priority patent/WO2007140061A2/en
Application filed by Research Foundation of the State University of New York filed Critical Research Foundation of the State University of New York
Priority to US12/301,963 priority Critical patent/US20100304983A1/en
Publication of WO2008134261A2 publication Critical patent/WO2008134261A2/en
Anticipated expiration legal-status Critical
Publication of WO2008134261A3 publication Critical patent/WO2008134261A3/en
Ceased legal-status Critical Current

Links

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
    • G16B15/00—ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
    • 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
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Engineering & Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biotechnology (AREA)
  • Medical Informatics (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Chemical & Material Sciences (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Analytical Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Peptides Or Proteins (AREA)
  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)

Abstract

An efficient computational method and system for predicting the folding regions and associated secondary and tertiary structures of a protein is disclosed. Methods and systems for sorting amino acid sequences based on predicted structures, as well as methods and systems for determining the presence or absence of genes in nucleic acid sequences or structural mutations in amino acid sequences are also disclosed. A method and system for the design of a protein is also disclosed.
PCT/US2008/060786 2007-04-27 2008-04-18 A method for protein structure determination, gene identification, mutational analysis, and protein design Ceased WO2008134261A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
US12/301,963 US20100304983A1 (en) 2007-04-27 2008-04-18 Method for protein structure determination, gene identification, mutational analysis, and protein design

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
PCT/US2007/067639 WO2007140061A2 (en) 2006-05-23 2007-04-27 A method for determining and predicting protein autonomous folding
USPCT/US2007/0067639 2007-04-27

Publications (2)

Publication Number Publication Date
WO2008134261A2 WO2008134261A2 (en) 2008-11-06
WO2008134261A3 true WO2008134261A3 (en) 2009-12-30

Family

ID=39930731

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2008/060786 Ceased WO2008134261A2 (en) 2007-04-27 2008-04-18 A method for protein structure determination, gene identification, mutational analysis, and protein design

Country Status (1)

Country Link
WO (1) WO2008134261A2 (en)

Families Citing this family (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2011100395A1 (en) * 2010-02-11 2011-08-18 The Research Foundation Of State University Of New York Computational methods for protein structure determination
CN112480204A (en) * 2020-04-13 2021-03-12 南京大学 Protein/polypeptide sequencing method adopting Aerolysin nanopores
CN114649052B (en) * 2022-03-22 2024-10-25 山东省计算中心（国家超级计算济南中心） RNA structure prediction method and system based on supercomputer Internet
CN116486906B (en) * 2023-04-17 2024-03-19 深圳新锐基因科技有限公司 Methods and devices for improving protein molecular stability based on amino acid residue mutations

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030130797A1 (en) * 1999-01-27 2003-07-10 Jeffrey Skolnick Protein modeling tools
US20050130224A1 (en) * 2002-05-31 2005-06-16 Celestar Lexico- Sciences, Inc. Interaction predicting device

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030130797A1 (en) * 1999-01-27 2003-07-10 Jeffrey Skolnick Protein modeling tools
US20050130224A1 (en) * 2002-05-31 2005-06-16 Celestar Lexico- Sciences, Inc. Interaction predicting device

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
AVBELJ ET AL.: "Prediction of the Three-Dimensional Structure of Proteins Using the Electrostatic Screening Model and Hierarchic Condensation.", PROTEINS: STRUCTURE, FUNCTION, AND GENETICS, vol. 31, 1998, pages 74 - 96 *

Also Published As

Publication number Publication date
WO2008134261A2 (en) 2008-11-06

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