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 | Acesso ao texto completo restrito à biblioteca da Embrapa Agricultura Digital. Para informações adicionais entre em contato com cnptia.biblioteca@embrapa.br. |
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Registro Completo |
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Biblioteca(s): |
Embrapa Agricultura Digital. |
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Data corrente: |
22/12/2015 |
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Data da última atualização: |
07/01/2020 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
NESHICH, I. A. P.; NISHIMURA, L.; MORAES, F. R. de; SALIM, J. A.; VILLALTA-ROMERO, F.; BORRO, L.; YANO, I. H.; MAZONI, I.; TASIC, L.; JARDINE, J. G.; NESHICH, G. |
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Afiliação: |
IZABELLA AGOSTINHO PENA NESHICH, Unicamp; LETICIA NISHIMURA, IQSC-USP; FABIO ROGÉRIO DE MORAES, Unesp, Sao José do Rio Preto; JOSE AUGUSTO SALIM, Unicamp; FABIAN VILLALTA-ROMERO; LUIZ BORRO, Unicamp; INACIO HENRIQUE YANO, CNPTIA; IVAN MAZONI, CNPTIA; LJUBICA TASIC, IQ/Unicamp; JOSÉ GILBERTO JARDINE, CNPTIA; GORAN NESHICH, CNPTIA. |
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Título: |
Computational Biology tools for identifying specific ligand binding residues for novel agrochemical and drug design. |
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Ano de publicação: |
2015 |
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Fonte/Imprenta: |
Current Protein and Peptide Science, v. 16, n. 8, p. 701-717, 2015. |
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ISBN: |
10.2174/1389203716666150505234923 |
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Idioma: |
Inglês |
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Conteúdo: |
The term ?agrochemicals? is used in its generic form to represent a spectrum of pesticides, such as insecticides, fungicides or bactericides. They contain active components designed for optimized pest management and control, therefore allowing for economically sound and labor efficient agricultural production. A ?drug? on the other side is a term that is used for compounds designed for controlling human diseases. Although drugs are subjected to much more severe testing and regulation procedures before reaching the market, they might contain exactly the same active ingredient as certain agrochemicals, what is the case described in present work, showing how a small chemical compound might be used to control pathogenicity of Gram negative bacteria Xylella fastidiosa which devastates citrus plantations, as well as for control of, for example, meningitis in humans. It is also clear that so far the production of new agrochemicals is not benefiting as much from the in silico new chemical compound identification/discovery as pharmaceutical production. Rational drug design crucially depends on detailed knowledge of structural information about the receptor (target protein) and the ligand (drug/agrochemical). The interaction between the two molecules is the subject of analysis that aims to understand relationship between structure and function, mainly deciphering some fundamental elements of the nanoenvironment where the interaction occurs. In this work we will emphasize the role of understanding nanoenvironmental factors that guide recognition and interaction of target protein and its function modifier, an agrochemical or a drug. The repertoire of nanoenvironment descriptors is used for two selected and specific cases we have approached in order to offer a technological solution for some very important problems that needs special attention in agriculture: elimination of pathogenicity of a bacterium which is attacking citrus plants and formulation of a new fungicide. Finally, we also briefly describe a workflow which might be useful when research requires that model structures of target proteins are firstly generated (starting from genome sequences), followed by identification of ligand-target sites at the surface of those modeled structures, then application of procedures that adequately prepare both protein and ligand structures (the latter also involving filtration that satisfies acceptable adsorption/desorption/metabolism/excretion/toxicity [ADMET] parameters) for virtual high throughput screening (involving docking of ligands to indicated sites) and terminating by ranking of best pairs: target protein with selected ligand. MenosThe term ?agrochemicals? is used in its generic form to represent a spectrum of pesticides, such as insecticides, fungicides or bactericides. They contain active components designed for optimized pest management and control, therefore allowing for economically sound and labor efficient agricultural production. A ?drug? on the other side is a term that is used for compounds designed for controlling human diseases. Although drugs are subjected to much more severe testing and regulation procedures before reaching the market, they might contain exactly the same active ingredient as certain agrochemicals, what is the case described in present work, showing how a small chemical compound might be used to control pathogenicity of Gram negative bacteria Xylella fastidiosa which devastates citrus plantations, as well as for control of, for example, meningitis in humans. It is also clear that so far the production of new agrochemicals is not benefiting as much from the in silico new chemical compound identification/discovery as pharmaceutical production. Rational drug design crucially depends on detailed knowledge of structural information about the receptor (target protein) and the ligand (drug/agrochemical). The interaction between the two molecules is the subject of analysis that aims to understand relationship between structure and function, mainly deciphering some fundamental elements of the nanoenvironment where the interaction occurs. In this work we will emphasize the role of u... Mostrar Tudo |
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Palavras-Chave: |
Agroquímicos; Bioinformática; Biology; Interaction nanoenvironment; Ligand docking; Nanoambiente; Protein-ligand interactions; Sting structure-function descriptors. |
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Thesagro: |
Biologia; Proteína. |
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Thesaurus Nal: |
Agrochemicals; Bioinformatics; Proteins. |
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Categoria do assunto: |
-- |
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Marc: |
LEADER 03817naa a2200397 a 4500
001 2032213
005 2020-01-07
008 2015 bl uuuu u00u1 u #d
100 1 $aNESHICH, I. A. P.
245 $aComputational Biology tools for identifying specific ligand binding residues for novel agrochemical and drug design.$h[electronic resource]
260 $c2015
520 $aThe term ?agrochemicals? is used in its generic form to represent a spectrum of pesticides, such as insecticides, fungicides or bactericides. They contain active components designed for optimized pest management and control, therefore allowing for economically sound and labor efficient agricultural production. A ?drug? on the other side is a term that is used for compounds designed for controlling human diseases. Although drugs are subjected to much more severe testing and regulation procedures before reaching the market, they might contain exactly the same active ingredient as certain agrochemicals, what is the case described in present work, showing how a small chemical compound might be used to control pathogenicity of Gram negative bacteria Xylella fastidiosa which devastates citrus plantations, as well as for control of, for example, meningitis in humans. It is also clear that so far the production of new agrochemicals is not benefiting as much from the in silico new chemical compound identification/discovery as pharmaceutical production. Rational drug design crucially depends on detailed knowledge of structural information about the receptor (target protein) and the ligand (drug/agrochemical). The interaction between the two molecules is the subject of analysis that aims to understand relationship between structure and function, mainly deciphering some fundamental elements of the nanoenvironment where the interaction occurs. In this work we will emphasize the role of understanding nanoenvironmental factors that guide recognition and interaction of target protein and its function modifier, an agrochemical or a drug. The repertoire of nanoenvironment descriptors is used for two selected and specific cases we have approached in order to offer a technological solution for some very important problems that needs special attention in agriculture: elimination of pathogenicity of a bacterium which is attacking citrus plants and formulation of a new fungicide. Finally, we also briefly describe a workflow which might be useful when research requires that model structures of target proteins are firstly generated (starting from genome sequences), followed by identification of ligand-target sites at the surface of those modeled structures, then application of procedures that adequately prepare both protein and ligand structures (the latter also involving filtration that satisfies acceptable adsorption/desorption/metabolism/excretion/toxicity [ADMET] parameters) for virtual high throughput screening (involving docking of ligands to indicated sites) and terminating by ranking of best pairs: target protein with selected ligand.
650 $aAgrochemicals
650 $aBioinformatics
650 $aProteins
650 $aBiologia
650 $aProteína
653 $aAgroquímicos
653 $aBioinformática
653 $aBiology
653 $aInteraction nanoenvironment
653 $aLigand docking
653 $aNanoambiente
653 $aProtein-ligand interactions
653 $aSting structure-function descriptors
700 1 $aNISHIMURA, L.
700 1 $aMORAES, F. R. de
700 1 $aSALIM, J. A.
700 1 $aVILLALTA-ROMERO, F.
700 1 $aBORRO, L.
700 1 $aYANO, I. H.
700 1 $aMAZONI, I.
700 1 $aTASIC, L.
700 1 $aJARDINE, J. G.
700 1 $aNESHICH, G.
773 $tCurrent Protein and Peptide Science$gv. 16, n. 8, p. 701-717, 2015.
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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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Biblioteca |
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| Registros recuperados : 34 | |
| 3. |  | BORRO, L. C.; SALIM, J. A.; MAZONI, I.; YANO, I.; JARDINE, J. G.; NESHICH, G. Improving binding affinity prediction by using a rule-based model with physical-chemical and structural descriptors of the nano-environment for protein-ligand interactions. In: CONGRESS OF THE INTERNATIONAL UNION FOR BIOCHEMISTRY AND MOLECULAR BIOLOGY, 23.; ANNUAL MEETING OF THE BRAZILIAN SOCIETY FOR BIOCHEMISTRY AND MOLECULAR BIOLOGY, 44., 2015, Foz do Iguaçu. Biochemistry for a better world: abstracts book. [Foz do Iguaçu]: SBBq, 2015. p. 153. C.047.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
|    |
| 4. | | SALIM, J. A.; BORRO, L.; MAZONI, I.; YANO, I. H.; JARDINE, J. G.; NESHICH, G. Multiple structure single parameter: analysis of a single protein nano environment descriptor characterizing a shared loci on structurally aligned proteins. Bioinformatics, v. 32, n. 12, p. 1885-1887, 2016.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Agricultura Digital. |
|  |
| 6. | | MAZONI, I.; BORRO, L. C.; JARDINE, J. G.; YANO, I. H.; SALIM, J. A.; NESHICH, G. Study of specific nanoenvironments containing [alfa]-helices in all-[alfa] and ([alfa]+[beta])+([alfa]/[beta]) proteins. Plos One, v. 13, n. 7, p. 1-25, 2018. Artigo e0200018.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Territorial. |
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| 8. | | JARDINE, J. G.; NESHICH, I. A. P.; MORAES, F. R. de; MAZONI, I.; MANCINI, A.; SALIM, J. A.; NESHICH, G. Generation of lipase B mutants with increased surface hydrophobicity in order to improve biodiesel catalysis. In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 5., 2009, Angra dos Reis. Abstracts book... Angra dos Reis: ABBCB, 2009. Não paginado. X-Meeting 2009.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 9. | | SALIM, J. A.; MAZONI, I.; MANCINI, A. L.; MORAES, F. R.; JARDINE, J. G.; NESHICH, I. P.; NESHICH, G. MSSP: a web-based application for analysis of selected parameter from multiple structures in a graphical manner. In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 5., 2009, Angra dos Reis. Abstracts book... Angra dos Reis: ABBCB, 2009. Não paginado. X-Meeting 2009.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 10. | | NESHICH, I. A. P.; MAZONI, I.; SALIM, J. A.; MORAES, F. R. de; NISHIMURA, L.; JARDINE, J. G.; NESHICH, G. Pathogenic Prion Proteins (PrP) have higher electrostatic potential pattern than normal cellular prion protein in a specific region. In: ANNUAL MEETING OF THE SBBq, 40., 2011, Foz do Iguaçu. [Proceedings...]. São Paulo, SP: Brazilian Society for Biochemistry and Molecular Biology, 2011. Não paginado.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 12. | | NESHICH, I. A. P.; MORAES, F. R. de; SALIM, J. A.; MAZONI, I.; MANCINI, A.; JARDINE, J. G.; NESHICH, G. Surface hydrophobicity index (SHI): insight into the mechanisms of protein-protein associations. In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 5., 2009, Angra dos Reis. Abstracts book... Angra dos Reis: ABBCB, 2009. Não paginado. X-Meeting 2009| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 13. | | MAZONI, I.; SALIM, J. A; NESHICH, I. A. P.; MORAES, F. R. de; NISHIMURA, L.; JARDINE, J. G.; NESHICH, G. Structure function relationship de convoluted to a level of physical chemical descriptors: case study - lysozyme / lactalbumine differences. In: ANNUAL MEETING OF THE SBBq, 40., 2011, Foz do Iguaçu. [Proceedings...]. São Paulo, SP: Brazilian Society for Biochemistry and Molecular Biology, 2011. Não paginado.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 14. | | NESHICH, I. A. P.; MORAES, F. de; SALIM, J. A.; MAZONI, I.; JARDINE, J. G.; NESHICH, G. Size matters: surface hydrophobicity index (SHI) describes the impact of the size of interface area on oligomerization driven by hydrophobic effect. In: ANNUAL INTERNATIONAL CONFERENCE ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY; STRUCTURAL BIOINFORMATICS AND COMPUTATIONAL BIOPHYSICS MEETING, 8., 2012, Long Beach, California. Abstracts... California: ISMB, 2012. Não paginado. 3Dsig 2012.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 15. | | JARDINE, J. G.; NESHICH, I. A. P.; MAZONI, I.; YANO, I. H.; MORAES, F. R. de; SALIM, J. A.; BORRO, L.; NISHIMURA, L. S.; NESHICH, G. Biologia computacional molecular e suas aplicações na agricultura. In: MASSRUHÁ, S. M. F. S.; LEITE, M. A. de A.; LUCHIARI JUNIOR, A.; ROMANI, L. A. S. (Ed.). Tecnologias da informação e comunicação e suas relações com a agricultura. Brasília, DF: Embrapa, 2014. Cap. 6. p. 101-117.| Tipo: Capítulo em Livro Técnico-Científico |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 16. | | SALIM, J. A.; VON ZUBEN, F. J.; MORAES, F. R. de; NESHICH, I. A. P.; MAZONI, I.; JARDINE, J.; NESHICH, G. Characterization of catalytic site residues using STING_DB structural descriptors. In: ANNUAL INTERNATIONAL CONFERENCE ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY; STRUCTURAL BIOINFORMATICS AND COMPUTATIONAL BIOPHYSICS CONFERENCE MEETING, 8., 2012, Long Beach, California. Abstracts... California: ISCB, 2012. Não paginado. Poster. 3DSIG 2012.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 17. | | MAZONI, I.; BORRO, L. C.; MANCINI, A.; SALIM, J. A.; MORAES, F. R.; JARDINE, J. G.; NESHICH, I. P.; NESHICH, G. Computational analysis of the secondary structure elements based on the physical chemical and geometrical descriptors and statistics data. In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 5., 2009, Angra dos Reis. Abstracts book... Angra dos Reis: ABBCB, 2009. Não paginado X-Meeting 2009.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 18. | | JARDINE, J. G.; NESHICH, I. A. P.; MAZONI, I.; YANO, I. H.; MORAES, F. R. de; SALIM, J. A; BORRO, L.; NISHIMURA, L. S.; NESHICH, G. Computational Molecular Biology and its applications in agriculture. In: MASSRUHÁ, S. M. F. S.; LEITE, M. A. de A.; LUCHIARI JUNIOR, A.; ROMANI, L. A. S. (Ed.). Information and communication technologies and their relations with agriculture. Brasília, DF: Embrapa, 2016. ch. 6, p. 103-118.| Tipo: Capítulo em Livro Técnico-Científico |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 19. | | MAZONI, I.; BORRO, L. C.; MANCINI, A.; SALIM, J. A.; MORAES, F. R.; JARDINE, J. G.; NESHICH, I. A. P.; NESHICH, G. Comparison between physical chemical and geometrical characteristics of the amino acids present in alpha-helices and beta-sheets. In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 5., 2009, Angra dos Reis. Abstracts book... Angra dos Reis: ABBCB, 2009. Não pagiando. X-Meeting 2009.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 20. | | KOFFLER, S.; SOARES, F. M.; GHILARDI-LOPES, N. P.; ALBERTINI, B.; DRUCKER, D. P.; SALIM, J. A.; NUNES-SILVA, P.; FRANCOY, T. M.; SARAIVA, A. M.; CARVELL, C. FIT Count Brasil: monitoramento de visitantes florais por contagem. Santo André, SP: Universidade Federal do ABC, 2022. 90 p. (Ciência cidadã, v. 7).| Tipo: Autoria/Organização/Edição de Livros |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| Registros recuperados : 34 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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