BRPI0513188A - métodos e sistemas para prever especificidades de ligação de proteìnas-ligantes - Google Patents

métodos e sistemas para prever especificidades de ligação de proteìnas-ligantes

Info

Publication number
BRPI0513188A
BRPI0513188A BRPI0513188-0A BRPI0513188A BRPI0513188A BR PI0513188 A BRPI0513188 A BR PI0513188A BR PI0513188 A BRPI0513188 A BR PI0513188A BR PI0513188 A BRPI0513188 A BR PI0513188A
Authority
BR
Brazil
Prior art keywords
protein
ligand binding
systems
methods
trained
Prior art date
Application number
BRPI0513188-0A
Other languages
English (en)
Inventor
Kodangattil R Sreekumar
Youping Huang
Mark H Pausch
Kamalakar Gulukota
Original Assignee
Wyeth Corp
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 Wyeth Corp filed Critical Wyeth Corp
Publication of BRPI0513188A publication Critical patent/BRPI0513188A/pt

Links

Classifications

    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
    • G01N33/502—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics for testing non-proliferative effects
    • G01N33/5041—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics for testing non-proliferative effects involving analysis of members of signalling pathways
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/566—Immunoassay; Biospecific binding assay; Materials therefor using specific carrier or receptor proteins as ligand binding reagents where possible specific carrier or receptor proteins are classified with their target compounds
    • 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
    • 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
    • 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
    • G16B40/20—Supervised data analysis
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
    • G01N2333/705—Assays involving receptors, cell surface antigens or cell surface determinants
    • G01N2333/72—Assays involving receptors, cell surface antigens or cell surface determinants for hormones
    • G01N2333/726—G protein coupled receptor, e.g. TSHR-thyrotropin-receptor, LH/hCG receptor, FSH
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2500/00—Screening for compounds of potential therapeutic value
    • 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

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Chemical & Material Sciences (AREA)
  • Immunology (AREA)
  • Medical Informatics (AREA)
  • Molecular Biology (AREA)
  • Biomedical Technology (AREA)
  • Theoretical Computer Science (AREA)
  • Analytical Chemistry (AREA)
  • Biophysics (AREA)
  • Hematology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Urology & Nephrology (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Data Mining & Analysis (AREA)
  • Evolutionary Computation (AREA)
  • Bioethics (AREA)
  • Public Health (AREA)
  • Pathology (AREA)
  • Epidemiology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Databases & Information Systems (AREA)
  • General Physics & Mathematics (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Biochemistry (AREA)
  • Cell Biology (AREA)
  • Software Systems (AREA)
  • Microbiology (AREA)
  • Artificial Intelligence (AREA)
  • Food Science & Technology (AREA)
  • Medicinal Chemistry (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Toxicology (AREA)
  • Genetics & Genomics (AREA)

Abstract

MéTODOS E SISTEMAS PARA PREVER ESPECIFICIDADES DE LIGAçãO DE PROTEìNAS-LIGANTES. A invenção refere-as a métodos e sistemas para prever e avaliar especificidades de ligações de proteínas-ligantes. Um modelo de reconhecimento de padrões pode ser treinado por segmentos de seqüências selecionados de proteínas de treinamento as quais têm uma especificidade de ligação de ligante especifico. Acredita-se que cada segmento de seqüência selecionado inclua um ou mais resíduos aminoácidos que podem contribuir para a especificidade de ligação de ligante da proteína de treinamento correspondente. Segmentos de seqüências em uma proteína de interesse podem ser similarmente selecionados e usados para inquirir o modelo treinado para determinar se a proteína de interesse tem a mesma especificidade de ligação de ligante que as proteínas de treinamento. Em uma modalidade, o modelo de reconhecimento de padrões empregado é um modelo de Markov oculto o qual é treinado por domínios citosálicos concatenados de GPCRs os quais têm preferência de interação com uma classe específica de proteínas G. Este modelo treinado pode ser usado para avaliar a especificidade de ligação de proteínas G de GPCRs órfãos.
BRPI0513188-0A 2004-07-09 2005-07-08 métodos e sistemas para prever especificidades de ligação de proteìnas-ligantes BRPI0513188A (pt)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US58640904P 2004-07-09 2004-07-09
PCT/US2005/024276 WO2006017181A2 (en) 2004-07-09 2005-07-08 Methods and systems for predicting protein-ligand coupling specificities

Publications (1)

Publication Number Publication Date
BRPI0513188A true BRPI0513188A (pt) 2008-04-29

Family

ID=35839753

Family Applications (1)

Application Number Title Priority Date Filing Date
BRPI0513188-0A BRPI0513188A (pt) 2004-07-09 2005-07-08 métodos e sistemas para prever especificidades de ligação de proteìnas-ligantes

Country Status (9)

Country Link
US (2) US20060008831A1 (pt)
EP (1) EP1782318A2 (pt)
JP (1) JP2008506120A (pt)
CN (1) CN101002206A (pt)
AU (1) AU2005271899A1 (pt)
BR (1) BRPI0513188A (pt)
CA (1) CA2571956A1 (pt)
MX (1) MXPA06014823A (pt)
WO (1) WO2006017181A2 (pt)

Families Citing this family (14)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
MX2013004548A (es) 2010-10-28 2013-07-05 Du Pont Plantas tolerantes a la sequia y constructos y metodos relacionados que involucran genes que codifican los polipeptidos dtp6.
US20150006532A1 (en) * 2012-01-18 2015-01-01 Dow Agrosciences Llc Stable pair-wise e-value
CN102760209A (zh) * 2012-05-17 2012-10-31 南京理工大学常熟研究院有限公司 一种非参数膜蛋白跨膜螺旋预测方法
CN103049678B (zh) * 2012-11-23 2015-09-09 中国科学院自动化研究所 基于蛋白质交互作用网络的异病同治分子机理分析方法
CN106232822A (zh) 2013-12-30 2016-12-14 纳幕尔杜邦公司 耐旱性植物和相关构建体及涉及编码dtp4多肽的基因的方法
CN104239751B (zh) * 2014-09-05 2017-11-14 南京理工大学 基于后处理学习的g蛋白偶联受体‑药物交互作用预测方法
CA2986810C (en) 2015-05-22 2024-01-02 Csts Health Care Inc. Thermodynamic measures on protein-protein interaction networks for cancer therapy
BR122023016256B8 (pt) 2015-08-06 2024-04-30 E I Du Pont De Nemours And Company Polipeptídeo inseticida recombinante, polinucleotídeo recombinante, construto de dna, método de obtenção de uma planta transgênica ou célula de planta transgênica, composição, proteína de fusão, método para controlar uma praga, método para inibir crescimento ou para exterminar uma população de pragas e uso do polipeptídeo
GB201607521D0 (en) * 2016-04-29 2016-06-15 Oncolmmunity As Method
CN108959852B (zh) * 2017-05-24 2021-12-24 北京工业大学 基于氨基酸-核苷酸成对偏好性信息的蛋白质上与rna结合模块的预测方法
CN107609340B (zh) * 2017-07-24 2020-05-05 浙江工业大学 一种多域蛋白距离谱构建方法
JP7168979B2 (ja) * 2019-01-31 2022-11-10 国立大学法人東京工業大学 立体構造判定装置、立体構造判定方法、立体構造の判別器学習装置、立体構造の判別器学習方法及びプログラム
EP3745404B1 (en) * 2019-05-29 2024-04-03 Cell Networks GmbH Method and system for predicting coupling probabilities of g-protein coupled receptors with g-proteins
CN114446383B (zh) * 2022-01-24 2023-04-21 电子科技大学 一种基于量子计算的配体-蛋白相互作用的预测方法

Also Published As

Publication number Publication date
JP2008506120A (ja) 2008-02-28
MXPA06014823A (es) 2007-02-12
US20060008831A1 (en) 2006-01-12
CN101002206A (zh) 2007-07-18
US20100293118A1 (en) 2010-11-18
CA2571956A1 (en) 2006-02-16
EP1782318A2 (en) 2007-05-09
WO2006017181A2 (en) 2006-02-16
AU2005271899A1 (en) 2006-02-16
WO2006017181A3 (en) 2006-09-21

Similar Documents

Publication Publication Date Title
BRPI0513188A (pt) métodos e sistemas para prever especificidades de ligação de proteìnas-ligantes
Leeming et al. A novel marker for assessment of liver matrix remodeling: an enzyme-linked immunosorbent assay (ELISA) detecting a MMP generated type I collagen neo-epitope (C1M)
Lei et al. Rare LRP6 variants identified in spina bifida patients
BR112012013330A2 (pt) composições e métodos para aumentar meia vida do soro de proteínas de fusão fc
Oblak et al. MD-2 determinants of nickel and cobalt-mediated activation of human TLR4
BRPI0514435B8 (pt) isolamento sequêncial de proteínas e esquemas de purificação através de cromatografia por afinidade
Pavelitz et al. PGBD5: a neural-specific intron-containing piggyBac transposase domesticated over 500 million years ago and conserved from cephalochordates to humans
BRPI0813898A2 (pt) métodos para selecionar um peptídeo ou polipeptídeo resistente à protease de um repertório de peptídeo ou polipeptídeos, para produzir um repertório de peptídeos ou polipeptídeos resistentes à protease, para fabricar um peptídeo ou polipeptídeo resistente à protease, e para tratar uma doença, peptídeo ou polipeptídeo resistente à protease, domínio variável simples de imunoglobulina resistente à protease isolada, antagonista, uso de um antagonista, ácido nucleico, vetor, e, célula hospedeira.
DK1864131T3 (da) Naturlig ligand af G protein koblet receptor RCC356 og anvendelser deraf
ZA200803403B (en) Botulinum neurotoxin a protein receptor and use thereof
BRPI0519429A2 (pt) composiÇço adequada para melhorar funÇço renal em um animal, mÉtodo para melhorar a funÇço renal em um animal, kit adequado para administrar composiÇÕes para melhorar a funÇço renal a um animal, meio para comunicar informaÇço, e, uso de uma composiÇço
NO20044051L (no) Analyse for ACTRIIB-kinase aktivitet
WO2005010215A3 (en) Methods for identifying tolerance modulatory compounds and uses therefor
Kenny et al. The Lophotrochozoan TGF-β signalling cassette-diversification and conservation in a key signalling pathway
WO2009068900A3 (en) Protein aggregation prediction systems
Rodriguez et al. Structural basis for substrate specificity of heteromeric transporters of neutral amino acids
Hernández González et al. A computer-aided approach for the discovery of D-peptides as inhibitors of SARS-CoV-2 main protease
ATE532072T1 (de) Verfahren und vorrichtung zur beurteilung von polypeptidaggregation
Smets et al. Evolutionary adaptation of the protein folding pathway for secretability
Leung et al. Unraveling the intricate microtubule inner protein networks that reinforce mammalian sperm flagella
US20140303010A1 (en) Methods and Compositions for Species-Specific Kinome Microarrays
Sallee et al. A pilot screen of a novel peptide hormone library identified candidate GPR83 ligands
BRPI0716767A2 (pt) mÉtodos para identificar uma proteÍna em uma amostra de proteÍna, e para isolar os peptÍdeos de terminal-c de uma amostra de proteÍna, base de dados, uso da mesma, e, dispositivo para identificar proteÍnas em uma ou mais amostras baseadas em seus peptÍdeos de terminal-c
ATE444757T1 (de) Verwendung der p2x7 antagonisten o-atp oder bbg zur behandlung von der neurodegerative phases des multiple sklerosis
Marsden et al. The Nkd EF-hand domain modulates divergent wnt signaling outputs in zebrafish

Legal Events

Date Code Title Description
B08F Application dismissed because of non-payment of annual fees [chapter 8.6 patent gazette]

Free format text: REFERENTE AS 5A, 6A E 7A ANUIDADES.

B08K Patent lapsed as no evidence of payment of the annual fee has been furnished to inpi [chapter 8.11 patent gazette]

Free format text: REFERENTE AO DESPACHO 8.6 PUBLICADO NA RPI 2158 DE 15/05/2012.