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| Registros recuperados : 120 | |
| 81. |  | MORAES, F. R. de; VILLANUEVA, W. J. P.; NESHICH, I. A. P.; MAZONI, I.; NISHIMURA, L.; SALIM, J. A.; JARDINE, J. G.; VON ZUBEN, F.; NESHICH, G. SIPEPPI, a systematic neuron network-based methodology for predicting protein-protein interfaces using STING database descriptors. In: ANNUAL MEETING OF THE SBBq, 40., 2011, Foz do Iguaçu. [Proceedings...]. São Paulo, SP: Brazilian Society for Biochemistry and Molecular Biology, 2011. Não paginado.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 82. | | MANCINI, A. L.; JARDINE, J. G.; MAZONI, I.; BORRO, L. C.; ALVARENGA, D.; CECILIO, P. L.; PELLIGRINELLI, T. V.; NESHICH, G. Structure descriptors of chameleon sequences. In: RED IBEROAMERICANA DE BIOINFORMÁTICA CONGRESS, 5., 2008, Chile. Program and abstracts... Santiago: Pontificia Universidad Católica de Chile, 2008. Não paginado. RIB 2008.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 84. | | JARDINE, J. G.; MAZONI, I.; MANCINI, A. L.; BORRO, L. C.; ALVARENGA, D.; CECÍLIO, P. L.; PELLIGRINELLI, T. V.; NESHICH, G. How did the structure function descriptors of proteins change with introduction of 'remediated' PDB files. In: RED IBEROAMERICANA DE BIOINFORMÁTICA CONGRESS, 5., 2008, Santiago. Program and abstracts... Santiago. Pontificia Universidade Católica de Chile, 2008. p. 15.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 85. | | 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. Improving predictions of protein-protein interfaces by combining amino acid-specific classifiers based on structural and physicochemical descriptors with their weighted neighbor averages. Plos One, San Francisco, v. 9, n. 1, p. 1-15, Jan. 2014.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 86. | | NARCISO, M. G.; YAMAGISHI, M. E. B.; QUINAGLIA, T.; SANTOS, E. H. dos; VIEIRA, F. D.; JARDINE, J. G.; MAZONI, I.; FALCAO, P. R. K.; NESHICH, G. Projeções de superfície 3D no plano para análise de interfaces proteicas através do Sting. Campinas: Embrapa Informática Agropecuária, 2006. 5 p. (Embrapa Informática Agropecuária. Comunicado técnico, 78). Na publicação: Goran Neshich.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 87. | | MAZONI, I.; SALIM, J. A.; YANO, I. H.; MORAES, F. R.; CARVALHO, J. G.; JARDINE, J. G.; NESHICH, I.; NESHICH, G. Prediction of a-helix using data mining decision tree technique. In: REUNIÃO ANUAL DA SOCIEDADE BRASILEIRA DE BIOQUÍMICA E BIOLOGIA MOLECULAR, 41., 2012, Foz do Iguaçu. Resumos... [S.l]: SBBq, 2012. Não paginado. Poster.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 88. | | FALCÃO, P. R. K.; MAZONI, I.; YAMAGISHI, M. E. B.; BORRO, L. C.; JARDINE, J. G.; SANTOS, E. H. dos; OLIVEIRA, S. R. de M.; NESHICH, G. Protein ligand contacts analyzed in an integrated environment with the other sequence and structure related parameters. In: ANNUAL INTERNATIONAL CONFERENCE ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY, 14.; ANNUAL AB3C CONFERENCE, 2., 2006, Fortaleza. Conference Program... Fortaleza: ISCB, 2006. Não paginado. Na publicação: Paula Kuser, Stanley R. M. Oliveira. ISMB, X-MEETING 2006. Poster I-49.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 89. | | NARCISO, M. G.; YAMAGISHI, M. E. B.; NESHICH, G.; FALCAO, P.; HENRIQUE, E.; VIEIRA, F. D.; JARDINE, J. G.; MAZONI, I. Transformação de imagens 3D para 2D para análise de proteínas usando o software Sting. In: CONGRESSO DE COMPUTAÇÃO DO SUL DE MATO GROSSO, 2., 2006, Rondonópolis. Computação e educação: anais. Rondonópolis: UFMT, 2006. p. 176-184. COMPSULMT 2006.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 90. | | MAZONI, I.; FALCÃO, P. R. K.; YAMAGISHI, M.; BORRO, L.; JARDINE, J. G.; SANTOS, E. H. dos; OLIVEIRA, S. R. de M.; NESHICH, G.; NARCISO, M. G. Comparisson of the amino acids co-evolution and the correlated structure descriptors. 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-51. Na publicação: Paula Kuser, Stanley R. M. Oliveira, Marcelo Narciso.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 91. | | MAZONI, I.; BORRO, L. C.; MANCINI, A.; SALIM, J. A.; MORAES, F. R.; JARDINE, J. G.; NESHICH, I. A. P.; NESHICH, G. Comparison between physical chemical and geometrical characteristics of the amino acids present in alpha-helices and beta-sheets. In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 5., 2009, Angra dos Reis. Abstracts book... Angra dos Reis: ABBCB, 2009. Não pagiando. X-Meeting 2009.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 92. | | KUSER, P.; YAMAGISHI, M. E. B.; OLIVEIRA, S. R. M.; MAZONI, I.; SANTOS, E. H. dos; VIEIRA, F. D.; JARDINE, J. G.; BORRO, L. C.; NESHICH, G. BlueStar STING - a multiplatform environment for protein structure analysis. 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-22. Na publicação: Paula Kuser, Stanley R. M. Oliveira, Edgard H. Santos.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 93. | | NARCISO, M. G.; YAMAGISHI, M. E. B.; QUINAGLIA, T.; SANTOS, E. H. dos; VIEIRA, F. D.; JARDINE, J. G.; MAZONI, I.; FALCAO, P. R. K.; NESHICH, G. Aspectos computacionais da análise da co-evolução de aminoácidos que pertencem a uma proteína qualquer. Campinas: Embrapa Informática Agropecuária, 2006. 4 p. (Embrapa Informática Agropecuária. Comunicado técnico, 77). Na publicação: Goran Neshich.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 94. | | NARCISO, M. G.; NESHICH, G.; YAMAGISHI, M. E. B.; FALCÃO, P.; SANTOS, E. H. dos; VIEIRA, F. D.; JARDINE, J. G.; MAZONI, I. Aspectos computacionais da análise da co-evolução de aminoácidos que pertencem a uma proteína qualquer usando o software Sting. In: CONGRESSO DE COMPUTAÇÃO DO SUL DE MATO GROSSO, 2., 2006, Rondonópolis. Computação e educação: anais. Rondonópolis: UFMT, 2006. p. 166-175. COMPSULMT 2006.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 95. | | JARDINE, J. G.; NESHICH, I. A. P.; MAZONI, I.; YANO, I. H.; MORAES, F. R. de; SALIM, J. A.; BORRO, L.; NISHIMURA, L. S.; NESHICH, G. Biologia computacional molecular e suas aplicações na agricultura. In: MASSRUHÁ, S. M. F. S.; LEITE, M. A. de A.; LUCHIARI JUNIOR, A.; ROMANI, L. A. S. (Ed.). Tecnologias da informação e comunicação e suas relações com a agricultura. Brasília, DF: Embrapa, 2014. Cap. 6. p. 101-117.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 96. | | MAZONI, I.; BORRO, L. C.; MANCINI, A.; SALIM, J. A.; MORAES, F. R.; JARDINE, J. G.; NESHICH, I. P.; NESHICH, G. Computational analysis of the secondary structure elements based on the physical chemical and geometrical descriptors and statistics data. In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 5., 2009, Angra dos Reis. Abstracts book... Angra dos Reis: ABBCB, 2009. Não paginado X-Meeting 2009.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 97. | | JARDINE, J. G.; NESHICH, I. A. P.; MAZONI, I.; YANO, I. H.; MORAES, F. R. de; SALIM, J. A; BORRO, L.; NISHIMURA, L. S.; NESHICH, G. Computational Molecular Biology and its applications in agriculture. In: MASSRUHÁ, S. M. F. S.; LEITE, M. A. de A.; LUCHIARI JUNIOR, A.; ROMANI, L. A. S. (Ed.). Information and communication technologies and their relations with agriculture. Brasília, DF: Embrapa, 2016. ch. 6, p. 103-118.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 98. | | SALIM, J. A.; MORAES, F. R. de; NESHICH, I. A. P.; MAZONI, I.; JARDINE, J. G.; VON ZUBEN, F.; NESHICH, G. A pattern recognition approach for catalytic site residues prediction using STING structural protein descriptors. In: REUNIÃO ANUAL DA SOCIEDADE BRASILEIRA DE BIOQUÍMICA E BIOLOGIA MOLECULAR, 41., 2012, Foz do Iguaçu. Resumos... [S.l]: SBBq, 2012. Não paginado. 1 pôster.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 99. | | JARDINE, J. G.; NESHICH, G.; FALCÃO, P. R. K.; YAMAGISHI, M. E. B.; OLIVEIRA, S. R. de M.; MARANGONI, S.; MARTINS, D.; WINCK, F. V.; NOVELLO, J. C. Molecular modeling of the protein twitching motility of Xylella fastidiosa. In: X-MEETING; INTERNATIONAL CONFERENCE OF THE AB3C, 1., 2005, Caxambu. [Proceedings...]. [S.l.]: Associação Brasileira de Bioinformática e Biologia Computacional, 2005. p. 99. Na publicação: Stanley R. M. Oliveira. X-meeting 2005. Presented Posters.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 100. | | JARDINE, J. G.; NESHICH, G.; MAZONI, I.; YANO, I. H.; NESHICH, I. P. A.; SALIM, J. A; DE MORAES, F. R. Molecular modeling and structural analysis of the protein twitching motility of Xylella fastidiosa. In: CONGRESSO BRASILEIRO DE BIOTECNOLOGIA E RODADA E FEIRA DE NEGÓCIOS, 4., 2012, Guarujá. [Resumos]... [S.l.: s.n.], 2012. Não paginado. Brasil Biotec 2012.| Biblioteca(s): Embrapa Agricultura Digital. |
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| Registros recuperados : 120 | |
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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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Circulação/Nível: |
A - 1 |
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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. |
|
Ano de publicação: |
2014 |
|
Fonte/Imprenta: |
Plos One, San Francisco, v. 9, n. 1, p. 1-15, Jan. 2014. |
|
ISBN: |
10.1371/journal.pone.0087107 |
|
Idioma: |
Inglês |
|
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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