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| Registros recuperados : 34 | |
| 3. |  | BORRO, L. C.; SALIM, J. A.; MAZONI, I.; YANO, I.; JARDINE, J. G.; NESHICH, G. Improving binding affinity prediction by using a rule-based model with physical-chemical and structural descriptors of the nano-environment for protein-ligand interactions. In: CONGRESS OF THE INTERNATIONAL UNION FOR BIOCHEMISTRY AND MOLECULAR BIOLOGY, 23.; ANNUAL MEETING OF THE BRAZILIAN SOCIETY FOR BIOCHEMISTRY AND MOLECULAR BIOLOGY, 44., 2015, Foz do Iguaçu. Biochemistry for a better world: abstracts book. [Foz do Iguaçu]: SBBq, 2015. p. 153. C.047.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 4. | | SALIM, J. A.; BORRO, L.; MAZONI, I.; YANO, I. H.; JARDINE, J. G.; NESHICH, G. Multiple structure single parameter: analysis of a single protein nano environment descriptor characterizing a shared loci on structurally aligned proteins. Bioinformatics, v. 32, n. 12, p. 1885-1887, 2016.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 7. | | MAZONI, I.; BORRO, L. C.; JARDINE, J. G.; YANO, I. H.; SALIM, J. A.; NESHICH, G. Study of specific nanoenvironments containing [alfa]-helices in all-[alfa] and ([alfa]+[beta])+([alfa]/[beta]) proteins. Plos One, v. 13, n. 7, p. 1-25, 2018. Artigo e0200018.| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Territorial. |
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| 8. | | 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.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 9. | | 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.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 10. | | 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.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 11. | | 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.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 13. | | 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.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 14. | | 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 2009| Biblioteca(s): Embrapa Agricultura Digital. |
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| 15. | | 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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| 16. | | 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.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 17. | | 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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| 18. | | 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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| 19. | | KOFFLER, S.; SOARES, F. M.; GHILARDI-LOPES, N. P.; ALBERTINI, B.; DRUCKER, D. P.; SALIM, J. A.; NUNES-SILVA, P.; FRANCOY, T. M.; SARAIVA, A. M.; CARVELL, C. FIT Count Brasil: monitoramento de visitantes florais por contagem. Santo André, SP: Universidade Federal do ABC, 2022. 90 p. (Ciência cidadã, v. 7).| Biblioteca(s): Embrapa Agricultura Digital. |
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| 20. | | 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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| Registros recuperados : 34 | |
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 | Acesso ao texto completo restrito à biblioteca da Embrapa Agricultura Digital. Para informações adicionais entre em contato com cnptia.biblioteca@embrapa.br. |
Registro Completo
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Biblioteca(s): |
Embrapa Agricultura Digital. |
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Data corrente: |
26/11/2009 |
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Data da última atualização: |
15/01/2020 |
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Tipo da produção científica: |
Resumo em Anais de Congresso |
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Autoria: |
MAZONI, I.; BORRO, L. C.; MANCINI, A.; SALIM, J. A.; MORAES, F. R.; JARDINE, J. G.; NESHICH, I. A. P.; NESHICH, G. |
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Afiliação: |
IVAN MAZONI, CNPTIA; LUIZ CÉSAR BORRO, Estagiário/CNPTIA; ADAUTO LUIZ MANCINI, CNPTIA; JOSÉ AUGUSTO SALIM, Estagiário/CNPTIA; FABIO ROGERIO DE MORAES, Bolsista/CNPTIA; JOSE GILBERTO JARDINE, CNPTIA; IZABELLA AGOSTINHO PENA NESHICH, Estagiária/CNPTIA; GORAN NESHICH, CNPTIA. |
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Título: |
Comparison between physical chemical and geometrical characteristics of the amino acids present in alpha-helices and beta-sheets. |
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Ano de publicação: |
2009 |
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Fonte/Imprenta: |
In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 5., 2009, Angra dos Reis. Abstracts book... Angra dos Reis: ABBCB, 2009. |
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Páginas: |
Não pagiando. |
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Idioma: |
Inglês |
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Notas: |
X-Meeting 2009. |
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Conteúdo: |
JSSD is software developed on the Java programming language, to analyze the secondary structure elements of the proteins. This analysis is based on the information about the amino acids physical chemical and geometrical parameters and allows characterize the functional proteins nanoenvironment, where the nucleation of secondary structure elements (alpha-helix, beta-sheets and loops) occurs (composed by initiation, propagation and termination). JSSD uses a database containing 720 different descriptors for each amino acid in any protein deposited in the PDB. Considering that each protein has 2 chains with 300 amino acids each one and there are more than 60000 structures deposited in the PDB, our database has 720 x 2 x 300 x 60,000 = 25,920,000,000 registers approximately. A first experiment was done with 40,710 proteins. We created data marts (extracts from PDB based on strict rules for selecting a particular characteristic) from these structures for the proteins families: all-alpha, all-beta and alpha + beta. Using only the amino acids sequence matching the initial and final position at selected secondary structure element and that has consensus on all three identifiers PDB, DSSP and Stride, the experiment showed that there are 34,095 alpha-helices on the all-alpha protein family; 8,645 beta-sheets on the all-beta protein family and 306,556 alpha-helices and 250,674 beta-sheets on the alpha + beta protein family (both secondary structure element of variable size starting from minimum 5 amino acids). MenosJSSD is software developed on the Java programming language, to analyze the secondary structure elements of the proteins. This analysis is based on the information about the amino acids physical chemical and geometrical parameters and allows characterize the functional proteins nanoenvironment, where the nucleation of secondary structure elements (alpha-helix, beta-sheets and loops) occurs (composed by initiation, propagation and termination). JSSD uses a database containing 720 different descriptors for each amino acid in any protein deposited in the PDB. Considering that each protein has 2 chains with 300 amino acids each one and there are more than 60000 structures deposited in the PDB, our database has 720 x 2 x 300 x 60,000 = 25,920,000,000 registers approximately. A first experiment was done with 40,710 proteins. We created data marts (extracts from PDB based on strict rules for selecting a particular characteristic) from these structures for the proteins families: all-alpha, all-beta and alpha + beta. Using only the amino acids sequence matching the initial and final position at selected secondary structure element and that has consensus on all three identifiers PDB, DSSP and Stride, the experiment showed that there are 34,095 alpha-helices on the all-alpha protein family; 8,645 beta-sheets on the all-beta protein family and 306,556 alpha-helices and 250,674 beta-sheets on the alpha + beta protein family (both secondary structure element of variable size starting from... Mostrar Tudo |
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Palavras-Chave: |
Bioinformática; Geometrical amino acids; Sting. |
|
Thesaurus NAL: |
Bioinformatics; Computer software. |
|
Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
|
Marc: |
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100 1 $aMAZONI, I.
245 $aComparison between physical chemical and geometrical characteristics of the amino acids present in alpha-helices and beta-sheets.$h[electronic resource]
260 $aIn: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 5., 2009, Angra dos Reis. Abstracts book... Angra dos Reis: ABBCB$c2009
300 $aNão pagiando.
500 $aX-Meeting 2009.
520 $aJSSD is software developed on the Java programming language, to analyze the secondary structure elements of the proteins. This analysis is based on the information about the amino acids physical chemical and geometrical parameters and allows characterize the functional proteins nanoenvironment, where the nucleation of secondary structure elements (alpha-helix, beta-sheets and loops) occurs (composed by initiation, propagation and termination). JSSD uses a database containing 720 different descriptors for each amino acid in any protein deposited in the PDB. Considering that each protein has 2 chains with 300 amino acids each one and there are more than 60000 structures deposited in the PDB, our database has 720 x 2 x 300 x 60,000 = 25,920,000,000 registers approximately. A first experiment was done with 40,710 proteins. We created data marts (extracts from PDB based on strict rules for selecting a particular characteristic) from these structures for the proteins families: all-alpha, all-beta and alpha + beta. Using only the amino acids sequence matching the initial and final position at selected secondary structure element and that has consensus on all three identifiers PDB, DSSP and Stride, the experiment showed that there are 34,095 alpha-helices on the all-alpha protein family; 8,645 beta-sheets on the all-beta protein family and 306,556 alpha-helices and 250,674 beta-sheets on the alpha + beta protein family (both secondary structure element of variable size starting from minimum 5 amino acids).
650 $aBioinformatics
650 $aComputer software
653 $aBioinformática
653 $aGeometrical amino acids
653 $aSting
700 1 $aBORRO, L. C.
700 1 $aMANCINI, A.
700 1 $aSALIM, J. A.
700 1 $aMORAES, F. R.
700 1 $aJARDINE, J. G.
700 1 $aNESHICH, I. A. P.
700 1 $aNESHICH, G.
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