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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: |
26/11/2009 |
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Data da última atualização: |
15/01/2020 |
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Tipo da produção científica: |
Resumo em Anais de Congresso |
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Autoria: |
MAZONI, I.; BORRO, L. C.; MANCINI, A.; SALIM, J. A.; MORAES, F. R.; JARDINE, J. G.; NESHICH, I. P.; NESHICH, G. |
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Afiliação: |
IVAN MAZONI, CNPTIA; L. C. BORRO, CNPTIA; ADAUTO LUIZ MANCINI, CNPTIA; JOSÉ AUGUSTO SALIM, Estagiário/CNPTIA; FABIO ROGERIO DE MORAES, Bolsista/CNPTIA; JOSE GILBERTO JARDINE, CNPTIA; IZABELLA PENA NESHICH, Estagiária/CNPTIA; GORAN NESHICH, CNPTIA. |
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Título: |
Computational analysis of the secondary structure elements based on the physical chemical and geometrical descriptors and statistics data. |
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Ano de publicação: |
2009 |
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Fonte/Imprenta: |
In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 5., 2009, Angra dos Reis. Abstracts book... Angra dos Reis: ABBCB, 2009. |
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Páginas: |
Não paginado |
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Idioma: |
Inglês |
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Notas: |
X-Meeting 2009. |
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Conteúdo: |
JSSD is software developed on the Java programming language, to analyze the secondary structure elements of the proteins. This analysis is based on the information about the amino acids physical chemical and geometrical parameters and allows characterize the functional proteins nanoenvironment, where the nucleation of secondary structure elements (alpha-helix, beta-sheets and loops) occurs (composed by initiation, propagation and termination). JSSD uses a database containing 720 different descriptors for each amino acid in any protein deposited in the PDB. Considering that each protein has 2 chains with 300 amino acids each one and there are more than 60000 structures deposited in the PDB, our database has 720 x 2 x 300 x 60,000 = 25,920,000,000 registers approximately. A first experiment was done with 40,710 proteins. We created data marts (extracts from PDB based on strict rules for selecting a particular characteristic) from these structures for the proteins families: all-alpha, all-beta and alpha + beta. Using only the amino acids sequence matching the initial and final position at selected secondary structure element and that has consensus on all three identifiers PDB, DSSP and Stride, the experiment showed that there are 34,095 alpha-helices on the all-alpha protein family; 8,645 beta-sheets on the all-beta protein family and 306,556 alpha-helices and 250,674 beta-sheets on the alpha + beta protein family (both secondary structure element of variable size starting from minimum 5 amino acids). MenosJSSD is software developed on the Java programming language, to analyze the secondary structure elements of the proteins. This analysis is based on the information about the amino acids physical chemical and geometrical parameters and allows characterize the functional proteins nanoenvironment, where the nucleation of secondary structure elements (alpha-helix, beta-sheets and loops) occurs (composed by initiation, propagation and termination). JSSD uses a database containing 720 different descriptors for each amino acid in any protein deposited in the PDB. Considering that each protein has 2 chains with 300 amino acids each one and there are more than 60000 structures deposited in the PDB, our database has 720 x 2 x 300 x 60,000 = 25,920,000,000 registers approximately. A first experiment was done with 40,710 proteins. We created data marts (extracts from PDB based on strict rules for selecting a particular characteristic) from these structures for the proteins families: all-alpha, all-beta and alpha + beta. Using only the amino acids sequence matching the initial and final position at selected secondary structure element and that has consensus on all three identifiers PDB, DSSP and Stride, the experiment showed that there are 34,095 alpha-helices on the all-alpha protein family; 8,645 beta-sheets on the all-beta protein family and 306,556 alpha-helices and 250,674 beta-sheets on the alpha + beta protein family (both secondary structure element of variable size starting from... Mostrar Tudo |
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Palavras-Chave: |
Análise computacional; Elementos de estrutura secundária; JSSD. |
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Thesagro: |
Dados Estatísticos. |
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Thesaurus Nal: |
Computer software. |
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Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
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Marc: |
LEADER 02508nam a2200277 a 4500
001 1576280
005 2020-01-15
008 2009 bl uuuu u00u1 u #d
100 1 $aMAZONI, I.
245 $aComputational analysis of the secondary structure elements based on the physical chemical and geometrical descriptors and statistics data.$h[electronic resource]
260 $aIn: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 5., 2009, Angra dos Reis. Abstracts book... Angra dos Reis: ABBCB$c2009
300 $aNão paginado
500 $aX-Meeting 2009.
520 $aJSSD is software developed on the Java programming language, to analyze the secondary structure elements of the proteins. This analysis is based on the information about the amino acids physical chemical and geometrical parameters and allows characterize the functional proteins nanoenvironment, where the nucleation of secondary structure elements (alpha-helix, beta-sheets and loops) occurs (composed by initiation, propagation and termination). JSSD uses a database containing 720 different descriptors for each amino acid in any protein deposited in the PDB. Considering that each protein has 2 chains with 300 amino acids each one and there are more than 60000 structures deposited in the PDB, our database has 720 x 2 x 300 x 60,000 = 25,920,000,000 registers approximately. A first experiment was done with 40,710 proteins. We created data marts (extracts from PDB based on strict rules for selecting a particular characteristic) from these structures for the proteins families: all-alpha, all-beta and alpha + beta. Using only the amino acids sequence matching the initial and final position at selected secondary structure element and that has consensus on all three identifiers PDB, DSSP and Stride, the experiment showed that there are 34,095 alpha-helices on the all-alpha protein family; 8,645 beta-sheets on the all-beta protein family and 306,556 alpha-helices and 250,674 beta-sheets on the alpha + beta protein family (both secondary structure element of variable size starting from minimum 5 amino acids).
650 $aComputer software
650 $aDados Estatísticos
653 $aAnálise computacional
653 $aElementos de estrutura secundária
653 $aJSSD
700 1 $aBORRO, L. C.
700 1 $aMANCINI, A.
700 1 $aSALIM, J. A.
700 1 $aMORAES, F. R.
700 1 $aJARDINE, J. G.
700 1 $aNESHICH, I. P.
700 1 $aNESHICH, G.
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