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Registro Completo |
Biblioteca(s): |
Embrapa Agricultura Digital. |
Data corrente: |
19/08/2013 |
Data da última atualização: |
22/05/2024 |
Tipo da produção científica: |
Artigo em Periódico Indexado |
Autoria: |
BOARETO, M.; YAMAGISHI, M. E. B.; CATICHA, N.; LEITE, V. B. P. |
Afiliação: |
MARCELO BOARETO, USP; MICHEL EDUARDO BELEZA YAMAGISHI, CNPTIA; NESTOR CATICHA, USP; VITOR B. P. LEITE, Unesp. |
Título: |
Relationship between global structural parameters and Enzyme Commission hierarchy: implications for function prediction. |
Ano de publicação: |
2012 |
Fonte/Imprenta: |
Computational Biology and Chemistry, Oxford, v. 40, p. 15-19, 2012. |
DOI: |
https://doi.org/10.1016/j.compbiolchem.2012.06.003 |
Idioma: |
Inglês |
Conteúdo: |
In protein databases there is a substantial number of proteins structurally determined but without function annotation. Understanding the relationship between function and structure can be useful to predict function on a large scale. We have analyzed the similarities in global physicochemical parameters for a set of enzymes which were classified according to the four Enzyme Commission (EC) hierarchical levels. Using relevance theory we introduced a distance between proteins in the space of physicochemical characteristics. This was done by minimizing a cost function of the metric tensor built to reflect the EC classification system. Using an unsupervised clustering method on a set of 1025 enzymes, we obtained no relevant clustering formation compatible with EC classification. The distance distributions between enzymes from the same EC group and from different EC groups were compared by histograms. Such analysis was also performed using sequence alignment similarity as a distance. Our results suggest that global structure parameters are not sufficient to segregate enzymes according to EC hierarchy. This indicates that features essential for function are rather local than global. Consequently, methods for predicting function based on global attributes should not obtain high accuracy in main EC classes prediction without relying on similarities between enzymes from training and validation datasets. Furthermore, these results are consistent with a substantial number of studies suggesting that function evolves fundamentally by recruitment, i.e., a same protein motif or fold can be used to perform different enzymatic functions and a few specific amino acids (AAs) are actually responsible for enzyme activity. These essential amino acids should belong to active sites and an effective method for predicting function should be able to recognize them. MenosIn protein databases there is a substantial number of proteins structurally determined but without function annotation. Understanding the relationship between function and structure can be useful to predict function on a large scale. We have analyzed the similarities in global physicochemical parameters for a set of enzymes which were classified according to the four Enzyme Commission (EC) hierarchical levels. Using relevance theory we introduced a distance between proteins in the space of physicochemical characteristics. This was done by minimizing a cost function of the metric tensor built to reflect the EC classification system. Using an unsupervised clustering method on a set of 1025 enzymes, we obtained no relevant clustering formation compatible with EC classification. The distance distributions between enzymes from the same EC group and from different EC groups were compared by histograms. Such analysis was also performed using sequence alignment similarity as a distance. Our results suggest that global structure parameters are not sufficient to segregate enzymes according to EC hierarchy. This indicates that features essential for function are rather local than global. Consequently, methods for predicting function based on global attributes should not obtain high accuracy in main EC classes prediction without relying on similarities between enzymes from training and validation datasets. Furthermore, these results are consistent with a substantial number of studies su... Mostrar Tudo |
Palavras-Chave: |
Bioinformática; Enzyme structure; Estrutura de enzimas; Function prediction; Parâmetros físico-químicos; Physicochemical parameters; Previsão de função. |
Thesaurus Nal: |
Bioinformatics. |
Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
Marc: |
LEADER 02766naa a2200265 a 4500 001 1964271 005 2024-05-22 008 2012 bl uuuu u00u1 u #d 024 7 $ahttps://doi.org/10.1016/j.compbiolchem.2012.06.003$2DOI 100 1 $aBOARETO, M. 245 $aRelationship between global structural parameters and Enzyme Commission hierarchy$bimplications for function prediction.$h[electronic resource] 260 $c2012 520 $aIn protein databases there is a substantial number of proteins structurally determined but without function annotation. Understanding the relationship between function and structure can be useful to predict function on a large scale. We have analyzed the similarities in global physicochemical parameters for a set of enzymes which were classified according to the four Enzyme Commission (EC) hierarchical levels. Using relevance theory we introduced a distance between proteins in the space of physicochemical characteristics. This was done by minimizing a cost function of the metric tensor built to reflect the EC classification system. Using an unsupervised clustering method on a set of 1025 enzymes, we obtained no relevant clustering formation compatible with EC classification. The distance distributions between enzymes from the same EC group and from different EC groups were compared by histograms. Such analysis was also performed using sequence alignment similarity as a distance. Our results suggest that global structure parameters are not sufficient to segregate enzymes according to EC hierarchy. This indicates that features essential for function are rather local than global. Consequently, methods for predicting function based on global attributes should not obtain high accuracy in main EC classes prediction without relying on similarities between enzymes from training and validation datasets. Furthermore, these results are consistent with a substantial number of studies suggesting that function evolves fundamentally by recruitment, i.e., a same protein motif or fold can be used to perform different enzymatic functions and a few specific amino acids (AAs) are actually responsible for enzyme activity. These essential amino acids should belong to active sites and an effective method for predicting function should be able to recognize them. 650 $aBioinformatics 653 $aBioinformática 653 $aEnzyme structure 653 $aEstrutura de enzimas 653 $aFunction prediction 653 $aParâmetros físico-químicos 653 $aPhysicochemical parameters 653 $aPrevisão de função 700 1 $aYAMAGISHI, M. E. B. 700 1 $aCATICHA, N. 700 1 $aLEITE, V. B. P. 773 $tComputational Biology and Chemistry, Oxford$gv. 40, p. 15-19, 2012.
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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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Biblioteca(s): |
Embrapa Acre. |
Data corrente: |
12/04/2006 |
Data da última atualização: |
16/11/2023 |
Tipo da produção científica: |
Resumo em Anais de Congresso |
Autoria: |
LEDO, F. J. da S.; CASALI, V. W. D.; CRUZ, C. D.; PEREIRA, P. R. G. |
Afiliação: |
FRANCISCO JOSE DA SILVA LEDO, CPAF-AC; VICENTE WAGNER DIAS CASALI, UFV; COSME DAMIÃO CRUZ, UFV; PAULO ROBERTO GOMES PEREIRA, UFV. |
Título: |
Análise genética em um dialelo de cultivares de alface. |
Ano de publicação: |
1999 |
Fonte/Imprenta: |
Genetics and Molecular Biology, Ribeirão Preto, v. 22, n. 3, 1999. Suplement. |
Idioma: |
Português |
Notas: |
Edição do 45º congresso Nacional de Genética. |
Conteúdo: |
O uso de hibridação de cultivares e linhagens tem sido uma prática comum no melhoramento de plantas autógamas, possibilitando a recombinação gênica e a ampliação da variabilidade existente para produzir novo cultivares adaptados às diversas finalidades. |
Palavras-Chave: |
Análisis de dialelos; Dialelo de alface; Fitomejoramiento; Hibridación; Lactuca sativa L; Lechuga; Técnicas y protocolos genéticos. |
Thesagro: |
Alface; Cruzamento dialélico; Hibridação; Melhoramento genético vegetal. |
Thesaurus NAL: |
Diallel analysis; Genetic techniques and protocols; Hybridization; Lettuce; Plant breeding. |
Categoria do assunto: |
G Melhoramento Genético |
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/190701/1/12879.pdf
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Marc: |
LEADER 01340nam a2200349 a 4500 001 1504004 005 2023-11-16 008 1999 bl uuuu u00u1 u #d 100 1 $aLEDO, F. J. da S. 245 $aAnálise genética em um dialelo de cultivares de alface.$h[electronic resource] 260 $aGenetics and Molecular Biology, Ribeirão Preto, v. 22, n. 3, 1999. Suplement.$c1999 500 $aEdição do 45º congresso Nacional de Genética. 520 $aO uso de hibridação de cultivares e linhagens tem sido uma prática comum no melhoramento de plantas autógamas, possibilitando a recombinação gênica e a ampliação da variabilidade existente para produzir novo cultivares adaptados às diversas finalidades. 650 $aDiallel analysis 650 $aGenetic techniques and protocols 650 $aHybridization 650 $aLettuce 650 $aPlant breeding 650 $aAlface 650 $aCruzamento dialélico 650 $aHibridação 650 $aMelhoramento genético vegetal 653 $aAnálisis de dialelos 653 $aDialelo de alface 653 $aFitomejoramiento 653 $aHibridación 653 $aLactuca sativa L 653 $aLechuga 653 $aTécnicas y protocolos genéticos 700 1 $aCASALI, V. W. D. 700 1 $aCRUZ, C. D. 700 1 $aPEREIRA, P. R. G.
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