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Registro Completo |
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Biblioteca(s): |
Embrapa Agricultura Digital. |
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Data corrente: |
07/12/2007 |
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Data da última atualização: |
11/05/2017 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
ROCCHIA, W.; NESHICH, G. |
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Afiliação: |
Scuola Normale Superiore, Italy; GORAN NESHICH, CNPTIA. |
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Título: |
Electrostatic potential calculation for biomolecules - creating a database of pré-calculated values reported on a per residue basis for all PDB protein structures. |
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Ano de publicação: |
2007 |
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Fonte/Imprenta: |
Genetics and Molecular Research, v. 6, n. 4, p. 923-936, 2007. |
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Idioma: |
Inglês |
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Conteúdo: |
Abstract. STING and JavaProtein Dossier provide a collection of physical-chemical parameters, describing protein structure, stability, function, and interaction, considered one of the most comprehensive among the available protein databases of similar type. Particular attention in STING is paid to the electrostatic potential. It makes use of DelPhi, a well-known tool that calculates this physical-chemical quantity for biomolecules by solving the Poisson Boltzmann equation. In this paper, we describe a modification to the DelPhi program aimed at integrating it within the STING environment. We also outline how the "amino acid electrostatic potential" and the "surface amino acid electrostatic potential" are calculated (over all Protein Data Bank (PDB) content) and how the corresponding values are made searchable in STING_DB. In addition, we show that the STING and JavaProtein Dossier are also capable of providing these particular parameter values for the analysis of protein structures modeled in computers or being experimentally solved, but not yet deposited in the PDB. Furthermore, we compare the calculated electrostatic potential values obtained by using the earlier version of DelPhi and those by STING, for the biologically relevant case of lysozyme-antibody interaction. Finally, we describe the STING capacity to make queries (at both residue and atomic levels) across the whole PDB, by looking at a specific case where the electrostatic potential parameter plays a crucial role in terms of a particular protein function, such as ligand binding. MenosAbstract. STING and JavaProtein Dossier provide a collection of physical-chemical parameters, describing protein structure, stability, function, and interaction, considered one of the most comprehensive among the available protein databases of similar type. Particular attention in STING is paid to the electrostatic potential. It makes use of DelPhi, a well-known tool that calculates this physical-chemical quantity for biomolecules by solving the Poisson Boltzmann equation. In this paper, we describe a modification to the DelPhi program aimed at integrating it within the STING environment. We also outline how the "amino acid electrostatic potential" and the "surface amino acid electrostatic potential" are calculated (over all Protein Data Bank (PDB) content) and how the corresponding values are made searchable in STING_DB. In addition, we show that the STING and JavaProtein Dossier are also capable of providing these particular parameter values for the analysis of protein structures modeled in computers or being experimentally solved, but not yet deposited in the PDB. Furthermore, we compare the calculated electrostatic potential values obtained by using the earlier version of DelPhi and those by STING, for the biologically relevant case of lysozyme-antibody interaction. Finally, we describe the STING capacity to make queries (at both residue and atomic levels) across the whole PDB, by looking at a specific case where the electrostatic potential parameter plays a crucial role... Mostrar Tudo |
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Palavras-Chave: |
Banco de dados; Bioinformática; Biomoléculas; Electrostatic potential of biomolecules; Protein structure analysis; Sting. |
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Thesagro: |
Proteína. |
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Thesaurus Nal: |
Bioinformatics; Protein structure. |
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Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
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URL: |
https://www.alice.cnptia.embrapa.br/alice/bitstream/doc/899/1/APElectrostaticStingGMR2007.pdf
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Marc: |
LEADER 02370naa a2200241 a 4500
001 1000899
005 2017-05-11
008 2007 bl uuuu u00u1 u #d
100 1 $aROCCHIA, W.
245 $aElectrostatic potential calculation for biomolecules - creating a database of pré-calculated values reported on a per residue basis for all PDB protein structures.$h[electronic resource]
260 $c2007
520 $aAbstract. STING and JavaProtein Dossier provide a collection of physical-chemical parameters, describing protein structure, stability, function, and interaction, considered one of the most comprehensive among the available protein databases of similar type. Particular attention in STING is paid to the electrostatic potential. It makes use of DelPhi, a well-known tool that calculates this physical-chemical quantity for biomolecules by solving the Poisson Boltzmann equation. In this paper, we describe a modification to the DelPhi program aimed at integrating it within the STING environment. We also outline how the "amino acid electrostatic potential" and the "surface amino acid electrostatic potential" are calculated (over all Protein Data Bank (PDB) content) and how the corresponding values are made searchable in STING_DB. In addition, we show that the STING and JavaProtein Dossier are also capable of providing these particular parameter values for the analysis of protein structures modeled in computers or being experimentally solved, but not yet deposited in the PDB. Furthermore, we compare the calculated electrostatic potential values obtained by using the earlier version of DelPhi and those by STING, for the biologically relevant case of lysozyme-antibody interaction. Finally, we describe the STING capacity to make queries (at both residue and atomic levels) across the whole PDB, by looking at a specific case where the electrostatic potential parameter plays a crucial role in terms of a particular protein function, such as ligand binding.
650 $aBioinformatics
650 $aProtein structure
650 $aProteína
653 $aBanco de dados
653 $aBioinformática
653 $aBiomoléculas
653 $aElectrostatic potential of biomolecules
653 $aProtein structure analysis
653 $aSting
700 1 $aNESHICH, G.
773 $tGenetics and Molecular Research$gv. 6, n. 4, p. 923-936, 2007.
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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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| Registros recuperados : 331 | |
| 2. |  | VIZZOTTO, M. Aspectos sobre benefícios à saúde do consumo. In: ANTUNES, L. E. C.; HOFFMANN, A. (Ed.). Pequenas frutas: o produtor pergunta, a Embrapa responde. Brasília, DF: Embrapa, 2012. p. 179-184. il. (Coleção 500 perguntas, 500 respostas).| Tipo: Capítulo em Livro Técnico-Científico |
| Biblioteca(s): Embrapa Clima Temperado. |
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| 6. | | VIZZOTTO, M. Características funcionais. In: ANTUNES, L. E. C.; REISSER JUNIOR, C.; SCHWENGBER, J. E. (Ed.). Morangueiro. Pelotas: Embrapa Clima Temperado: Brasília, DF: Embrapa, 2016. 589 p. p. 563-571| Tipo: Capítulo em Livro Técnico-Científico |
| Biblioteca(s): Embrapa Clima Temperado. |
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| 8. | | VIZZOTTO, M. Mirtilo. In: DONADIO, L. C.; ZACCARO, R. P. Valor nutricional de frutas. Jaboticabal : SBF / Coopercitrus, 2012. 248 p.| Tipo: Capítulo em Livro Técnico-Científico |
| Biblioteca(s): Embrapa Clima Temperado. |
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| 9. | | VIZZOTTO, M. Propriedades funcionais do butiá. In: SIMPÓSIO NACIONAL DO MORANGO, 5.; ENCONTRO SOBRE PEQUENAS FRUTAS E FRUTAS NATIVAS DO MERCOSUL, 4., 2010, Pelotas. Palestras e resumos... Pelotas: Embrapa Clima Temperado, 2010. p. 139-140| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Clima Temperado. |
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| 12. | | VIZZOTTO, M. Pitanga: uma fruta especial. Jornal da fruta, Lages, v. 195, p. 23, fev, 2008. Publicado também no Jornal Toda Fruta <http://www.todafruta.com.br/todafruta/mostra_conteudo.asp?conteudo=16591> e no Jornal Diário da Manhã, Pelotas, p. 7, 23 dez. 2007.| Tipo: Artigo de Divulgação na Mídia |
| Biblioteca(s): Embrapa Clima Temperado. |
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| 13. | | VIZZOTTO, M. Pêssego: composição e benefícios à saúde. In: RASEIRA, M. do C. B.; PEREIRA, J. F. M.; CARVALHO, F. L. C. (ed.). Cultivo do pessegueiro. Pelotas: Embrapa Clima Temperado, 2022. (Embrapa Clima Temperado. Sistemas de Produção, 4). ODS. p. 167-172.| Tipo: Capítulo em Livro Técnico-Científico |
| Biblioteca(s): Embrapa Clima Temperado. |
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| 16. | | VIZZOTTO, M.; VINHOLES, J. R. Benefícios à saúde. In: MAYER, N. A.; FRANZON, R. C.; RASEIRA, M. do C. B. (Ed.). Pêssego, nectarina e ameixa: o produtor pergunta, a Embrapa responde. Brasília, DF: Embrapa, 2019. 290 p. il. (Coleção 500 perguntas, 500 respostas). cap. 19. p.283-290| Tipo: Capítulo em Livro Técnico-Científico |
| Biblioteca(s): Embrapa Clima Temperado. |
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| Registros recuperados : 331 | |
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