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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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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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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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| Registros recuperados : 7 | |
| 1. |  | MELO, R. C.; MAZONI, I.; NESHICH, G.; SANTORO, M. M.; MEIRA JÚNIOR, W. Contacts as the key elements for comparing two protein structures. In: ANNUAL INTERNATIONAL CONFERENCE ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY, 14.; ANNUAL AB3C CONFERENCE, 2., 2006, Fortaleza. Conference Program... Fortaleza: ISCB, 2006. Não paginado. ISMB, X-MEETING 2006. Poster I-6.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 2. | | MELO, R. C.; MAZONI, I.; NESHICH, G.; SANTORO, M. M.; MEIRA JUNIOR, W. Protein structure topology comparison based on contact maps. In: ANNUAL INTERNATIONAL CONFERENCE ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY, 14.; ANNUAL AB3C CONFERENCE, 2., 2006, Fortaleza. Conference Program... Fortaleza: ISCB, 2006. Não paginado. ISMB, X-MEETING 2006. Poster I-5.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 4. | | MELO, R. C.; GOMIDE, J. S.; MEIRA JUNIOR, W.; LOPES, J. C. D.; NESHICH, G.; SANTORO, M. M. Mining structural signatures in proteins using intrachain interactions. In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 3., 2007, São Paulo. Proceedings... Campinas: Embrapa Informática Agropecuária, 2007. p. 133. X-meeting 2007.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 5. | | GOMIDE, J.; MELO-MINARDI, R.; SANTOS, M. A. dos; NESHICH, G.; MEIRA JUNIOR, W.; LOPES, J. C.; SANTORO, M. Using linear algebra for protein structural comparison and classification. Genetics and Molecular Biology, v. 32, n. 3, p. 645-651, 2009.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 1 |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 6. | | MELO, R. C.; RIBEIRO, C.; MURRAY, C. S.; VELOSO, C. J. M.; SILVEIRA, C. H. da; NESHICH, G.; MEIRA JUNIOR, W.; CARCERONI, R. L.; SANTORO, M. M. Finding protein-protein interaction patterns by contact map matching. Genetics and Molecular Research, v. 6, n. 4, p. 946-963, 2007.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: Internacional - A |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 7. | | SILVEIRA, C. H. da; PIRES, D. E. V.; MINARDI, R.; RIBEIRO, C.; VELOSO, C. J. M.; LOPES, J. C. D.; MEIRA JÚNIOR, W.; NESHICH, G.; RAMOS, C. H. I.; HABESCH, R.; SANTORO, M. M. Protein cutoff scanning: a comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins. Proteins, n. 74, p. 727-743, 2009.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| Registros recuperados : 7 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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