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| 7. |  | REICHERT, J. M.; ALBUQUERQUE, J. A.; GUBIANI, P. I.; KAISER, D. R.; MINELLA, J. P. G.; REINERT, D. J. Hidrologia do solo, disponibilidade de água às plantas e zoneamento agroclimático. Tópicos em Ciência do Solo, Viçosa, MG, v. 7, p. 1-54, 2011.| Biblioteca(s): Embrapa Semiárido. |
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| 8. | | SOARES, J. C. W.; REINERT, D. J.; REICHERT, J. M.; KAISER, D. R.; MINELLA, J. P. G.; GONÇALVES, A. D. M. de A.; SILVA, T. A.; ALMEIDA NETTO, T.; BRESSAN, V. C. Relação solo/paisagem e sua variação temporal em uma estação experimental de silvicultura. Ciência Florestal, Santa Maria, v. 25, n. 2, p. 477-489, abr./jun. 2015. Nota técnica.| Biblioteca(s): Embrapa Florestas. |
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Registro Completo
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Biblioteca(s): |
Embrapa Agricultura Digital. |
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Data corrente: |
15/04/2010 |
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Data da última atualização: |
29/09/2016 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Circulação/Nível: |
B - 1 |
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Autoria: |
GOMIDE, J.; MELO-MINARDI, R.; SANTOS, M. A. dos; NESHICH, G.; MEIRA JUNIOR, W.; LOPES, J. C.; SANTORO, M. |
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Afiliação: |
JANAÍNA GOMIDE, UFMG; RAQUEL MELO-MINARDI, UFMG; MARCOS AUGUSTO DOS SANTOS, UFMG; GORAN NESHICH, CNPTIA; WAGNER MEIRA JUNIOR, UFMG; JÚLIO CÉSAR LOPES, UFMG; MARCELO SANTORO, UFMG. |
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Título: |
Using linear algebra for protein structural comparison and classification. |
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Ano de publicação: |
2009 |
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Fonte/Imprenta: |
Genetics and Molecular Biology, v. 32, n. 3, p. 645-651, 2009. |
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DOI: |
http://dx.doi.org/10.1590/S1415-47572009000300032 |
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Idioma: |
Inglês |
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Conteúdo: |
In this article, we describe a novel methodology to extract semantic characteristics from protein structures using linear algebra in order to compose structural signature vectors which may be used efficiently to compare and classify protein structures into fold families. These signatures are built from the pattern of hydrophobic intrachain interactions using Singular Value Decomposition (SVD) and Latent Semantic Indexing (LSI) techniques. Considering proteins as documents and contacts as terms, we have built a retrieval system which is able to find conserved contacts in samples of myoglobin fold family and to retrieve these proteins among proteins of varied folds with precision of up to 80%. The classifier is a web tool available at our laboratory website. Users can search for similar chains from a specific PDB, view and compare their contact maps and browse their structures using a JMol plug-in. |
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Palavras-Chave: |
Contact maps; Latent semantic indexing; Linear algebra; Protein classification; Singular value decomposition. |
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Thesagro: |
Biologia molecular. |
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Thesaurus NAL: |
Molecular biology. |
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Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/147910/1/AP-UsingLinearAlgebra-Gomide-2009.pdf
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Marc: |
LEADER 01799naa a2200289 a 4500
001 1664383
005 2016-09-29
008 2009 bl uuuu u00u1 u #d
024 7 $ahttp://dx.doi.org/10.1590/S1415-47572009000300032$2DOI
100 1 $aGOMIDE, J.
245 $aUsing linear algebra for protein structural comparison and classification.$h[electronic resource]
260 $c2009
520 $aIn this article, we describe a novel methodology to extract semantic characteristics from protein structures using linear algebra in order to compose structural signature vectors which may be used efficiently to compare and classify protein structures into fold families. These signatures are built from the pattern of hydrophobic intrachain interactions using Singular Value Decomposition (SVD) and Latent Semantic Indexing (LSI) techniques. Considering proteins as documents and contacts as terms, we have built a retrieval system which is able to find conserved contacts in samples of myoglobin fold family and to retrieve these proteins among proteins of varied folds with precision of up to 80%. The classifier is a web tool available at our laboratory website. Users can search for similar chains from a specific PDB, view and compare their contact maps and browse their structures using a JMol plug-in.
650 $aMolecular biology
650 $aBiologia molecular
653 $aContact maps
653 $aLatent semantic indexing
653 $aLinear algebra
653 $aProtein classification
653 $aSingular value decomposition
700 1 $aMELO-MINARDI, R.
700 1 $aSANTOS, M. A. dos
700 1 $aNESHICH, G.
700 1 $aMEIRA JUNIOR, W.
700 1 $aLOPES, J. C.
700 1 $aSANTORO, M.
773 $tGenetics and Molecular Biology$gv. 32, n. 3, p. 645-651, 2009.
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Embrapa Agricultura Digital (CNPTIA) |
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