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Registro Completo |
Biblioteca(s): |
Embrapa Agricultura Digital. |
Data corrente: |
25/02/2014 |
Data da última atualização: |
20/05/2014 |
Tipo da produção científica: |
Artigo em Periódico Indexado |
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. |
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. |
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 |
Palavras-Chave: |
Interações proteína-proteína. |
Thesagro: |
Biologia. |
Thesaurus Nal: |
Biological sciences; Proteins. |
Categoria do assunto: |
S Ciências Biológicas |
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/98207/1/journal.pone.0087107.pdf
|
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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Registros recuperados : 30 | |
3. | ![Imagem marcado/desmarcado](/consulta/web/img/desmarcado.png) | BRANDÃO, M.; ARRUDA, L.; MOURA, D.; SILVA FILHO, M.; SILVA, F. H. da; MALAGÓ JÚNIOR, W.; NESHICH, I.; NESHICH, G. Milho: manobra de escape. Cultivar Grandes Culturas, v. 18, n. 146, p. 6-7, jul., 2011.Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 5 |
Biblioteca(s): Embrapa Agricultura Digital; Embrapa Pecuária Sudeste. |
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4. | ![Imagem marcado/desmarcado](/consulta/web/img/desmarcado.png) | NESHICH, I. A. P.; MAZONI, I.; SALIM, J. A.; MORAES, F. R. de; NISHIMURA, L.; JARDINE, J. G.; NESHICH, G. Pathogenic Prion Proteins (PrP) have higher electrostatic potential pattern than normal cellular prion protein in a specific region. 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.Tipo: Resumo em Anais de Congresso |
Biblioteca(s): Embrapa Agricultura Digital. |
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5. | ![Imagem marcado/desmarcado](/consulta/web/img/desmarcado.png) | SALIM, J. A.; MAZONI, I.; MANCINI, A. L.; MORAES, F. R.; JARDINE, J. G.; NESHICH, I. P.; NESHICH, G. MSSP: a web-based application for analysis of selected parameter from multiple structures in a graphical manner. 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.Tipo: Resumo em Anais de Congresso |
Biblioteca(s): Embrapa Agricultura Digital. |
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6. | ![Imagem marcado/desmarcado](/consulta/web/img/desmarcado.png) | JARDINE, J. G.; NESHICH, I. A. P.; MORAES, F. R. de; MAZONI, I.; MANCINI, A.; SALIM, J. A.; NESHICH, G. Generation of lipase B mutants with increased surface hydrophobicity in order to improve biodiesel catalysis. 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.Tipo: Resumo em Anais de Congresso |
Biblioteca(s): Embrapa Agricultura Digital. |
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7. | ![Imagem marcado/desmarcado](/consulta/web/img/desmarcado.png) | NESHICH, I. A. P.; MORAES, F. R. de; SALIM, J. A.; MAZONI, I.; MANCINI, A.; JARDINE, J. G.; NESHICH, G. Surface hydrophobicity index (SHI): insight into the mechanisms of protein-protein associations. 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 2009Tipo: Resumo em Anais de Congresso |
Biblioteca(s): Embrapa Agricultura Digital. |
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8. | ![Imagem marcado/desmarcado](/consulta/web/img/desmarcado.png) | MAZONI, I.; SALIM, J. A; NESHICH, I. A. P.; MORAES, F. R. de; NISHIMURA, L.; JARDINE, J. G.; NESHICH, G. Structure function relationship de convoluted to a level of physical chemical descriptors: case study - lysozyme / lactalbumine differences. 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.Tipo: Resumo em Anais de Congresso |
Biblioteca(s): Embrapa Agricultura Digital. |
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9. | ![Imagem marcado/desmarcado](/consulta/web/img/desmarcado.png) | NESHICH, I. A. P.; MORAES, F. de; SALIM, J. A.; MAZONI, I.; JARDINE, J. G.; NESHICH, G. Size matters: surface hydrophobicity index (SHI) describes the impact of the size of interface area on oligomerization driven by hydrophobic effect. In: ANNUAL INTERNATIONAL CONFERENCE ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY; STRUCTURAL BIOINFORMATICS AND COMPUTATIONAL BIOPHYSICS MEETING, 8., 2012, Long Beach, California. Abstracts... California: ISMB, 2012. Não paginado. 3Dsig 2012.Tipo: Resumo em Anais de Congresso |
Biblioteca(s): Embrapa Agricultura Digital. |
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10. | ![Imagem marcado/desmarcado](/consulta/web/img/desmarcado.png) | 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.Tipo: Capítulo em Livro Técnico-Científico |
Biblioteca(s): Embrapa Agricultura Digital. |
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11. | ![Imagem marcado/desmarcado](/consulta/web/img/desmarcado.png) | 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.Tipo: Resumo em Anais de Congresso |
Biblioteca(s): Embrapa Agricultura Digital. |
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12. | ![Imagem marcado/desmarcado](/consulta/web/img/desmarcado.png) | 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.Tipo: Capítulo em Livro Técnico-Científico |
Biblioteca(s): Embrapa Agricultura Digital. |
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13. | ![Imagem marcado/desmarcado](/consulta/web/img/desmarcado.png) | SALIM, J. A.; VON ZUBEN, F. J.; MORAES, F. R. de; NESHICH, I. A. P.; MAZONI, I.; JARDINE, J.; NESHICH, G. Characterization of catalytic site residues using STING_DB structural descriptors. In: ANNUAL INTERNATIONAL CONFERENCE ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY; STRUCTURAL BIOINFORMATICS AND COMPUTATIONAL BIOPHYSICS CONFERENCE MEETING, 8., 2012, Long Beach, California. Abstracts... California: ISCB, 2012. Não paginado. Poster. 3DSIG 2012.Tipo: Resumo em Anais de Congresso |
Biblioteca(s): Embrapa Agricultura Digital. |
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14. | ![Imagem marcado/desmarcado](/consulta/web/img/desmarcado.png) | 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.Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
Biblioteca(s): Embrapa Agricultura Digital. |
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15. | ![Imagem marcado/desmarcado](/consulta/web/img/desmarcado.png) | DIAS-LOPES, C.; NESHICH, I. A. P.; NESHICH, G.; ORTEGA, J. M.; GRANIER, C.; CHÁVEZ-OLORTEGUI, C.; MOLINA, F.; FELICORI, L. Identification of new Sphingomyelinases D in pathogenic fungi and other pathogenic organisms. PLoS ONE, San Francisco, v. 8, n. 11, p. 1-12, 2013.Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
Biblioteca(s): Embrapa Agricultura Digital. |
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16. | ![Imagem marcado/desmarcado](/consulta/web/img/desmarcado.png) | CAMPEIRO, J. D'A.; NESHICH, I. P.; SANT'ANNA, O. A.; LOPES, R.; IANZER, D.; ASSAKURA, M. T.; NESHICH, G.; HAYASHI, M. A. F. Identification of snake bradykinin-potentiating peptides (BPPs)-simile sequences in rat brain: potential BPP-like precursor protein? Biochemical Pharmacology, New York, v. 96, n. 3, p. 202-215, Aug. 2015.Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
Biblioteca(s): Embrapa Agricultura Digital. |
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17. | ![Imagem marcado/desmarcado](/consulta/web/img/desmarcado.png) | 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.Tipo: Resumo em Anais de Congresso |
Biblioteca(s): Embrapa Agricultura Digital. |
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18. | ![Imagem marcado/desmarcado](/consulta/web/img/desmarcado.png) | DUARTE, F.; SEPULVEDA, R.; ARAYA, R.; FLORES, S.; PEREZ-ACLE, T.; GONZALES, W.; GONZALES, D.; NESHICH, G.; NESHICH, I.; MAZONI, I.; HOLMES, D. S. Mechanisms of protein stabilization at very low pH. In: INTERNATIONAL BIOHYDROMETALLURGY SYMPOSIUM, 19.; 2011, Changsha, China. Biohydrometallurgy: biotech key to unlock mineral resources value: proceedings. Changsha: Central South University Press, 2011. v. 1. IBS 2011.Tipo: Artigo em Anais de Congresso |
Biblioteca(s): Embrapa Agricultura Digital. |
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19. | ![Imagem marcado/desmarcado](/consulta/web/img/desmarcado.png) | BRAGHINI, C. A.; NESHICH, I. A. P.; NESHICH, G.; SOARDI, F. C.; MELLO, M. P. de; COSTA, V. P.; VASCONCELLOS, J. P. C. de; MELO, M. B. de. New mutation in the myocilin gene segregates with juvenile-onset open-angle glaucoma in a Brazilian family Gene, Amsterdam, v. 535, n. 1, p. 50-57, July 2013.Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
Biblioteca(s): Embrapa Agricultura Digital. |
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20. | ![Imagem marcado/desmarcado](/consulta/web/img/desmarcado.png) | 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.Tipo: Resumo em Anais de Congresso |
Biblioteca(s): Embrapa Agricultura Digital. |
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Registros recuperados : 30 | |
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