[go: up one dir, main page]

WO2001092990A3 - Structure-based methods for assessing amino acid variances - Google Patents

Structure-based methods for assessing amino acid variances Download PDF

Info

Publication number
WO2001092990A3
WO2001092990A3 PCT/US2001/017351 US0117351W WO0192990A3 WO 2001092990 A3 WO2001092990 A3 WO 2001092990A3 US 0117351 W US0117351 W US 0117351W WO 0192990 A3 WO0192990 A3 WO 0192990A3
Authority
WO
WIPO (PCT)
Prior art keywords
amino acid
protein
methods
based methods
interest
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/US2001/017351
Other languages
French (fr)
Other versions
WO2001092990A2 (en
Inventor
Daniel I Chasman
R Mark Adams
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.)
Nuvelo Inc
Original Assignee
Variagenics 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
Application filed by Variagenics Inc filed Critical Variagenics Inc
Priority to AU2001265131A priority Critical patent/AU2001265131A1/en
Priority to JP2002501137A priority patent/JP2004501446A/en
Priority to CA002410726A priority patent/CA2410726A1/en
Priority to EP01939635A priority patent/EP1350115A2/en
Publication of WO2001092990A2 publication Critical patent/WO2001092990A2/en
Anticipated expiration legal-status Critical
Publication of WO2001092990A3 publication Critical patent/WO2001092990A3/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
    • 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
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/20—Sequence assembly
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Engineering & Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Medical Informatics (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Peptides Or Proteins (AREA)

Abstract

Variance modeling and prediction methods that are useful for assessing whether an amino acid variation at a selected amino acid residue in a protein of interest is likely (or is not likely) to have an effect on the protein (e.g., alter a biological activity of the protein) are described. The methods can be used to generate a structural model or models of all or a part of the protein of interest, assess the quality of the structural model, and evaluate the potential functional consequences of an amino acid variation. The methods achieve these goals by considering certain functional, structural, and phylogenetic features of specific amino acid residues.
PCT/US2001/017351 2000-06-01 2001-05-30 Structure-based methods for assessing amino acid variances Ceased WO2001092990A2 (en)

Priority Applications (4)

Application Number Priority Date Filing Date Title
AU2001265131A AU2001265131A1 (en) 2000-06-01 2001-05-30 Structure-based methods for assessing amino acid variances
JP2002501137A JP2004501446A (en) 2000-06-01 2001-05-30 Structure-based methods for assessing amino acid diversity
CA002410726A CA2410726A1 (en) 2000-06-01 2001-05-30 Structure-based methods for assessing amino acid variances
EP01939635A EP1350115A2 (en) 2000-06-01 2001-05-30 Structure-based methods for assessing amino acid variances

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US20862800P 2000-06-01 2000-06-01
US60/208,628 2000-06-01
US61473500A 2000-07-12 2000-07-12
US09/614,735 2000-07-12

Publications (2)

Publication Number Publication Date
WO2001092990A2 WO2001092990A2 (en) 2001-12-06
WO2001092990A3 true WO2001092990A3 (en) 2003-07-31

Family

ID=26903348

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/017351 Ceased WO2001092990A2 (en) 2000-06-01 2001-05-30 Structure-based methods for assessing amino acid variances

Country Status (5)

Country Link
EP (1) EP1350115A2 (en)
JP (1) JP2004501446A (en)
AU (1) AU2001265131A1 (en)
CA (1) CA2410726A1 (en)
WO (1) WO2001092990A2 (en)

Families Citing this family (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9493753B2 (en) 2011-03-16 2016-11-15 Amano Enzyme Inc. Modified α-glucosidase and applications of same
CN110223730B (en) * 2019-06-06 2022-09-27 河南师范大学 Prediction method and prediction device for protein and small molecule binding site
CN111128300B (en) * 2019-12-26 2023-03-24 上海市精神卫生中心（上海市心理咨询培训中心） Protein interaction influence judgment method based on mutation information
CN112257917B (en) * 2020-10-19 2023-05-12 北京工商大学 Time sequence abnormal mode detection method based on entropy characteristics and neural network

Non-Patent Citations (7)

* Cited by examiner, † Cited by third party
Title
CHASMAN DANIEL ET AL: "Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: Structure-based assessment of amino acid variation.", JOURNAL OF MOLECULAR BIOLOGY, vol. 307, no. 2, 2001, pages 683 - 706, XP002212639, ISSN: 0022-2836 *
DATABASE BIOSIS [online] BIOSCIENCES INFORMATION SERVICE, PHILADELPHIA, PA, US; 1994, ALTSCHUL STEPHEN F ET AL: "Issues in searching molecular sequence databases.", XP002212660, Database accession no. PREV199497283170 *
NATURE GENETICS, vol. 6, no. 2, 1994, pages 119 - 129, ISSN: 1061-4036 *
REDDY BOOJALA V B ET AL: "Use of propensities of amino acids to the local structural environments to understand effect of substitution mutations on protein stability.", PROTEIN ENGINEERING, vol. 11, no. 12, December 1998 (1998-12-01), pages 1137 - 1145, XP002212641, ISSN: 0269-2139 *
SUNYAEV SHAMIL ET AL: "Prediction of deleterious human alleles.", HUMAN MOLECULAR GENETICS, vol. 10, no. 6, 2001, pages 591 - 597, XP002212640, ISSN: 0964-6906 *
SUNYAEV SHAMIL ET AL: "Towards a structural basis of human non-synonymous single nucleotide polymorphisms.", TRENDS IN GENETICS, vol. 16, no. 5, May 2000 (2000-05-01), pages 198 - 200, XP002212759, ISSN: 0168-9525 *
WANG ZHEN ET AL: "SNPs, protein structure, and disease.", HUMAN MUTATION, vol. 17, no. 4, 2001, pages 263 - 270, XP001104863, ISSN: 1059-7794 *

Also Published As

Publication number Publication date
EP1350115A2 (en) 2003-10-08
AU2001265131A1 (en) 2001-12-11
CA2410726A1 (en) 2001-12-06
JP2004501446A (en) 2004-01-15
WO2001092990A2 (en) 2001-12-06

Similar Documents

Publication Publication Date Title
RU2316818C2 (en) Device for modeling inspiration, and device for modeling a spontaneous emotion, and corresponding methods and programs
WO2006078539A3 (en) System verification test using a behavior model
WO2005027717A3 (en) Bioimpedance methods and apparatus
WO2005034185A3 (en) System and method for on-tool semiconductor simulation
WO2005038560A3 (en) Method for providing physics simulation data
WO2006127144A3 (en) Adaptive customer assistance system for software products
WO2006129087A8 (en) Surgical system and method
WO2004042033A3 (en) Circulating stem cells and uses related thereto
WO2002067188A3 (en) Image analysis of the golgi complex
WO2004104769A3 (en) Methods and systems for computer-based neurocognitive testing
WO2007020598A3 (en) Method and apparatus featuring simple click style interactions according to a clinical task workflow
WO2007022020A3 (en) Dynamic healthcare modeling
WO2001092990A3 (en) Structure-based methods for assessing amino acid variances
ATE410677T1 (en) BIOEQUIVALENCE TEST FOR IRON-CONTAINING FORMULATIONS
WO2005012901A3 (en) Method for measuring aromatase activity
WO2008002941A3 (en) Analysis of heart rate variability data in animals for health condition assessment
WO2005109343A3 (en) Image data processing system for compartmental analysis
WO2006062542A3 (en) System and method for automatically generating a tooling specification using a logical operations utility that can be used to generate a photomask order
FI20031778A0 (en) The method, instrument, computer program, and system for providing feedback to the user during operation
Antoch et al. Detection of structural changes in generalized linear models
Satlin et al. Development of function in the metanephric kidney
Arnold et al. Modeling mixtures resulting from concurrent exposures to multiple sources
EP1179817A3 (en) Method and system for analyzing behavior of whole human body by simulation using whole human body model
WO2004048909A3 (en) Compressed vector-based spectral analysis method and system for nonlinear rf blocks
Blockley et al. Calibration commentary

Legal Events

Date Code Title Description
AK Designated states

Kind code of ref document: A2

Designated state(s): AE AG AL AM AT AU AZ BA BB BG BR BY BZ CA CH CN CR CU CZ DE DK DM DZ EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX MZ NO NZ PL PT RO RU SD SE SG SI SK SL TJ TM TR TT TZ UA UG US US UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: A2

Designated state(s): GH GM KE LS MW MZ SD SL SZ TZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE TR BF BJ CF CG CI CM GA GN GW ML MR NE SN TD TG

121 Ep: the epo has been informed by wipo that ep was designated in this application
DFPE Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101)
WWE Wipo information: entry into national phase

Ref document number: 2410726

Country of ref document: CA

WWE Wipo information: entry into national phase

Ref document number: 2001939635

Country of ref document: EP

ENP Entry into the national phase

Ref country code: JP

Ref document number: 2002 501137

Kind code of ref document: A

Format of ref document f/p: F

WWP Wipo information: published in national office

Ref document number: 2001939635

Country of ref document: EP

WWW Wipo information: withdrawn in national office

Ref document number: 2001939635

Country of ref document: EP