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| Registros recuperados : 38 | |
| 5. |  | RIBEIRO, C.; FALCAO, P. R. K.; NESHICH, G.; SANTORO, M. Serine proteases analysis based on phylogenetic trees constructed from the sequence and structure alignments. 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-48. Na publicação: Paula Kuser.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 7. | | 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.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 9. | | 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.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 10. | | 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.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 11. | | 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.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 12. | | SANTOS, A. M. C.; OLIVEIRA, J. S. de; BITTAR, E. R.; SILVA, A. L. da; GUIA, M. L. dos; BEMQUERER, M. P.; SANTORO, M. M. Improved purification process of β- and α-tripsin isoforms by ion-exchange choromatography. Brazilian Archives of Biology and technologgy: an International Journal, v.51, n. 4, p. 711-721, jul.-ago., 2008.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 13. | | 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.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 14. | | LIMA, F. L.; CARVALHO, M. A. R. de; APOLÔNIO, A. C. M.; BEMQUERER, M. P.; SANTORO, M. M.; OLIVEIRA, J. S.; ALVIANO, C. S.; FARIAS, L. de M. Actinomycetemcomitin: a new bacteriocin produced by Aggregatibacter (Actinobacillus) actinomycetemcomitans. Journal of Industrial Microbiology and Biotechnology, v. 35, p. 103-110, 2008.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 15. | | LIMA, F. L.; CARVALHO, M. A. R.; SANTORO, M. M.; BEMQUERER, M. P.; OLIVEIRA, J. S.; APOLÔNIO, A. C. M.; ALVIANO, C. S.; FARIAS, L. M. Actinomycetemcomitin: a new bacteriocin produced by Aggregatibacter (Actinobacillus) Actinomycetemcomitans. In: ANNUAL MEETING OF THE SBBq, 36.; IUBMB CONFERENCE, 10., 2007, Salvador, BA. Infectious diseases: biochemistry of parasites, vectors and hosts: program and abstracts. São Paulo, SP: Brazilian Society for Biochemistry and Molecular Biology, 2007.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 16. | | VIANA, P. A.; REZENDE, S. T. de; ALVES, A. de A.; MANFRINI, R. M.; ALVES, R. J.; BEMQUERER, M. P.; SANTORO, M. M.; GUIMARÃES, V. M. Activity of Debaryomyces hansenii UFV-1 alfa-galactosidades against alfa-D-galactophyranoside derivatives. Carbohydrate Research, v. 346, p. 602-605, 2011.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 17. | | PIMENTA, A. M. C.; RATES, B.; BLOCH JUNIOR, C.; GOMES, P. C.; SANTORO, M. M.; LIMA, M. E. de; RICHARDSON, M.; CORDEIRO, M. do N. Electrospray ionization quadrupole time-of-flight and matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometric analyses to solve micro heterogeneity in post-translationally modified peptides from Phoneutria nigriventer (Aranea, Ctenidae) venom. Rapid Communications in Mass Spectrometry, Chichester, UK, v. 19, p. 31-37, 2005.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 19. | | APOLÔNIO, A. C. M.; CARVALHO, M. A. R.; BEMQUERER, M. P.; SANTORO, M. M.; PINTO, S. Q.; OLIVEIRA, J. S.; SANTOS, K. V.; FARIAS, L. M. Purification and partial characterization of a bacteriocin produced by Eikenella corrodens. Journal of Applied Microbiology, v. 104, p. 508-514, 2008.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 20. | | SANTORO, M.; BROGIO, B. do A.; FORTE, M. J.; SOARES, M. R. R.; COLLUSSO, G. T.; JACOMINO, A. P.; SILVA, S. R. da. Vegetative multiplication of the Atlantic Rainforest species Eugenia involucrata. Pesquisa Agropecuária Brasileira, v. 57, e02921, 2022. Título em português: Multiplicação vegetativa da espécie Eugenia involucrata, nativa da Mata Atlântica.| Biblioteca(s): Embrapa Unidades Centrais. |
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| Registros recuperados : 38 | |
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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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