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Registro Completo |
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Biblioteca(s): |
Embrapa Agricultura Digital. |
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Data corrente: |
25/02/2014 |
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Data da última atualização: |
20/05/2014 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
MORAES, F. R. de; NESHICH, I. A. P.; MAZONI, I.; YANO, I. H.; PEREIRA, J. G. C.; SALIM, J. A.; JARDINE, J. G.; NESHICH, G. |
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Afiliação: |
FÁBIO R. DE MORAES, IB/Unicamp, CNPTIA; IZABELLA A. P. NESHICH, IB/Unicamp, CNPTIA; IVAN MAZONI, IB/Unicamp, CNPTIA; INÁCIO HENRIQUE YANO, CNPTIA; JOSÉ G. C. PEREIRA, IB/Unicamp, CNPTIA; JOSÉ A. SALIM, Unicamp; JOSE GILBERTO JARDINE, CNPTIA; GORAN NESHICH, CNPTIA. |
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Título: |
Improving predictions of protein-protein interfaces by combining amino acid-specific classifiers based on structural and physicochemical descriptors with their weighted neighbor averages. |
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Ano de publicação: |
2014 |
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Fonte/Imprenta: |
Plos One, San Francisco, v. 9, n. 1, p. 1-15, Jan. 2014. |
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ISBN: |
10.1371/journal.pone.0087107 |
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Idioma: |
Inglês |
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Conteúdo: |
Protein-protein interactions are involved in nearly all regulatory processes in the cell and are considered one of the most important issues in molecular biology and pharmaceutical sciences but are still not fully understood. Structural and computational biology contributed greatly to the elucidation of the mechanism of protein interactions. In this paper, we present a collection of the physicochemical and structural characteristics that distinguish interface-forming residues (IFR) from free surface residues (FSR). We formulated a linear discriminative analysis (LDA) classifier to assess whether chosen descriptors from the BlueStar STING database (http://www.cbi.cnptia.embrapa.br/SMS/) are suitable for such a task. Receiver operating characteristic (ROC) analysis indicates that the particular physicochemical and structural descriptors used for building the linear classifier perform much better than a random classifier and in fact, successfully outperform some of the previously published procedures, whose performance indicators were recently compared by other research groups. The results presented here show that the selected set of descriptors can be utilized to predict IFRs, even when homologue proteins are missing (particularly important for orphan proteins where no homologue is available for comparative analysis/indication) or, when certain conformational changes accompany interface formation. The development of amino acid type specific classifiers is shown to increase IFR classification performance. Also, we found that the addition of an amino acid conservation attribute did not improve the classification prediction. This result indicates that the increase in predictive power associated with amino acid conservation is exhausted by adequate use of an extensive list of independent physicochemical and structural parameters that, by themselves, fully describe the nano-environment at protein-protein interfaces. The IFR classifier developed in this study is now integrated into the BlueStar STING suite of programs. Consequently, the prediction of protein-protein interfaces for all proteins available in the PDB is possible through STING_interfaces module, accessible at the following website: (http://www.cbi.cnptia.embrapa.br/SMS/predictions/index.html). MenosProtein-protein interactions are involved in nearly all regulatory processes in the cell and are considered one of the most important issues in molecular biology and pharmaceutical sciences but are still not fully understood. Structural and computational biology contributed greatly to the elucidation of the mechanism of protein interactions. In this paper, we present a collection of the physicochemical and structural characteristics that distinguish interface-forming residues (IFR) from free surface residues (FSR). We formulated a linear discriminative analysis (LDA) classifier to assess whether chosen descriptors from the BlueStar STING database (http://www.cbi.cnptia.embrapa.br/SMS/) are suitable for such a task. Receiver operating characteristic (ROC) analysis indicates that the particular physicochemical and structural descriptors used for building the linear classifier perform much better than a random classifier and in fact, successfully outperform some of the previously published procedures, whose performance indicators were recently compared by other research groups. The results presented here show that the selected set of descriptors can be utilized to predict IFRs, even when homologue proteins are missing (particularly important for orphan proteins where no homologue is available for comparative analysis/indication) or, when certain conformational changes accompany interface formation. The development of amino acid type specific classifiers is shown to increase IFR... Mostrar Tudo |
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Palavras-Chave: |
Interações proteína-proteína. |
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Thesagro: |
Biologia. |
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Thesaurus Nal: |
Biological sciences; Proteins. |
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Categoria do assunto: |
S Ciências Biológicas |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/98207/1/journal.pone.0087107.pdf
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Marc: |
LEADER 03127naa a2200253 a 4500
001 1981215
005 2014-05-20
008 2014 bl uuuu u00u1 u #d
100 1 $aMORAES, F. R. de
245 $aImproving predictions of protein-protein interfaces by combining amino acid-specific classifiers based on structural and physicochemical descriptors with their weighted neighbor averages.$h[electronic resource]
260 $c2014
520 $aProtein-protein interactions are involved in nearly all regulatory processes in the cell and are considered one of the most important issues in molecular biology and pharmaceutical sciences but are still not fully understood. Structural and computational biology contributed greatly to the elucidation of the mechanism of protein interactions. In this paper, we present a collection of the physicochemical and structural characteristics that distinguish interface-forming residues (IFR) from free surface residues (FSR). We formulated a linear discriminative analysis (LDA) classifier to assess whether chosen descriptors from the BlueStar STING database (http://www.cbi.cnptia.embrapa.br/SMS/) are suitable for such a task. Receiver operating characteristic (ROC) analysis indicates that the particular physicochemical and structural descriptors used for building the linear classifier perform much better than a random classifier and in fact, successfully outperform some of the previously published procedures, whose performance indicators were recently compared by other research groups. The results presented here show that the selected set of descriptors can be utilized to predict IFRs, even when homologue proteins are missing (particularly important for orphan proteins where no homologue is available for comparative analysis/indication) or, when certain conformational changes accompany interface formation. The development of amino acid type specific classifiers is shown to increase IFR classification performance. Also, we found that the addition of an amino acid conservation attribute did not improve the classification prediction. This result indicates that the increase in predictive power associated with amino acid conservation is exhausted by adequate use of an extensive list of independent physicochemical and structural parameters that, by themselves, fully describe the nano-environment at protein-protein interfaces. The IFR classifier developed in this study is now integrated into the BlueStar STING suite of programs. Consequently, the prediction of protein-protein interfaces for all proteins available in the PDB is possible through STING_interfaces module, accessible at the following website: (http://www.cbi.cnptia.embrapa.br/SMS/predictions/index.html).
650 $aBiological sciences
650 $aProteins
650 $aBiologia
653 $aInterações proteína-proteína
700 1 $aNESHICH, I. A. P.
700 1 $aMAZONI, I.
700 1 $aYANO, I. H.
700 1 $aPEREIRA, J. G. C.
700 1 $aSALIM, J. A.
700 1 $aJARDINE, J. G.
700 1 $aNESHICH, G.
773 $tPlos One, San Francisco$gv. 9, n. 1, p. 1-15, Jan. 2014.
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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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Registro Completo
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Biblioteca(s): |
Embrapa Acre. |
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Data corrente: |
15/01/2008 |
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Data da última atualização: |
20/12/2023 |
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Tipo da produção científica: |
Resumo em Anais de Congresso |
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Autoria: |
MALVEIRA, C. L. de O.; BARROS, L. S. de; ALMEIDA, M. L. M. de; BRILHANTE, R. T.; PEREIRA, J. E. S.; FERMINO JÚNIOR, P. C. P. |
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Afiliação: |
CLÁUDIO LUIZ DE OLIVEIRA MALVEIRA, UFAC; LAUCIENY SANTANA DE BARROS, UFAC; MARIA LINDALVA MÁXIMO DE ALMEIDA, UFAC; RICARDO TEIXEIRA BRILHANTE, UFAC; JONNY EVERSON SCHERWINSKI PEREIRA, CPAF-AC; PAULO CESAR POETA FERMINO JÚNIOR, UFAC. |
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Título: |
Aspectos da anatomia foliar de ipê amarelo (Tabebuia serratifolia) no Acre. |
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Ano de publicação: |
2007 |
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Fonte/Imprenta: |
In: SEMINÁRIO DE INICIAÇÃO CIENTÍFICA PIBIC/CNPq//UFAC/EMBRAPA, 16.; MOSTRA DE PESQUISA E PÓS-GRADUAÇÃO, 6., 2007, Rio Branco, AC. A pesquisa e a pós-graduação contribuindo com o desenvolvimento da região: anais. Rio Branco, AC: Ufac, 2007. |
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Páginas: |
2 p. |
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Descrição Física: |
1 CD ROM. |
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Idioma: |
Português |
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Conteúdo: |
A Tabebuia serratifolia (Vahl) G. Nicholson, pertence à família Bignoniaceae, e é conhecida como Ipê-amarelo, ipê-do-cerrado, ipê-ovo-de-macuco, ipê-pardo, ipê-tabaco, ipê-uva, pau-d’arco e pau-d’arco-amarelo. Os ipês são extremamente ornamentais, e nos últimos anos têm sido utilizados na arborização de ruas e parques e em reflorestamentos, e a sua madeira pode ser empregada na construção civil. Alguns estudos anatômicos foliares já foram realizados para Tabebuia avellanedae e Tabebuia chrysotricha, porém são escassos os estudos com T. serratiflolia. O objetivo do trabalho foi descrever aspectos da anatomia de folhas de Tabebuia serratifolia disponibilizando dados taxonômicos para o gênero. |
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Palavras-Chave: |
Construção civil; Pau-d'arco. |
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Thesagro: |
Planta Ornamental; Taxonomia. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/doc/501083/1/16826.pdf
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Marc: |
LEADER 01619nam a2200229 a 4500
001 1501083
005 2023-12-20
008 2007 bl uuuu u00u1 u #d
100 1 $aMALVEIRA, C. L. de O.
245 $aAspectos da anatomia foliar de ipê amarelo (Tabebuia serratifolia) no Acre.$h[electronic resource]
260 $aIn: SEMINÁRIO DE INICIAÇÃO CIENTÍFICA PIBIC/CNPq//UFAC/EMBRAPA, 16.; MOSTRA DE PESQUISA E PÓS-GRADUAÇÃO, 6., 2007, Rio Branco, AC. A pesquisa e a pós-graduação contribuindo com o desenvolvimento da região: anais. Rio Branco, AC: Ufac$c2007
300 $a2 p.$c1 CD ROM.
520 $aA Tabebuia serratifolia (Vahl) G. Nicholson, pertence à família Bignoniaceae, e é conhecida como Ipê-amarelo, ipê-do-cerrado, ipê-ovo-de-macuco, ipê-pardo, ipê-tabaco, ipê-uva, pau-d’arco e pau-d’arco-amarelo. Os ipês são extremamente ornamentais, e nos últimos anos têm sido utilizados na arborização de ruas e parques e em reflorestamentos, e a sua madeira pode ser empregada na construção civil. Alguns estudos anatômicos foliares já foram realizados para Tabebuia avellanedae e Tabebuia chrysotricha, porém são escassos os estudos com T. serratiflolia. O objetivo do trabalho foi descrever aspectos da anatomia de folhas de Tabebuia serratifolia disponibilizando dados taxonômicos para o gênero.
650 $aPlanta Ornamental
650 $aTaxonomia
653 $aConstrução civil
653 $aPau-d'arco
700 1 $aBARROS, L. S. de
700 1 $aALMEIDA, M. L. M. de
700 1 $aBRILHANTE, R. T.
700 1 $aPEREIRA, J. E. S.
700 1 $aFERMINO JÚNIOR, P. C. P.
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Embrapa Acre (CPAF-AC) |
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