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Registros recuperados : 26 | |
5. | | MAZONI, I.; JARDINE, J. G.; BORRO, L. C.; ALVARENGA, D.; NESHICH, G. Electrostatic potential at the alpha carbon atoms along the alpha helices and beta strands. In: ANNUAL MEETING OF SBBQ, 37.; CONGRESS OF THE PAN-AMERICAN ASSOCIATION FOR BIOCHEMISTRY AND MOLECULAR BIOLOGY, 11, 2008, Águas de Lindóia. Program and index... Águas de Lindóia, Program and index... Águas de Lindóia: SBBq, 2008. Não paginado. PABMB. Biblioteca(s): Embrapa Agricultura Digital. |
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6. | | JARDINE, J. G.; MAZONI, I.; BORRO, L. C.; ALVARENGA, D.; NESHICH, G. Signature contact coordination patterns for secondary structure elements in protein structures. In: ANNUAL MEETING OF SBBQ, 37.; CONGRESS OF THE PAN-AMERICAN ASSOCIATION FOR BIOCHEMISTRY AND MOLECULAR BIOLOGY, 11, 2008, Águas de Lindóia. Program and index... Águas de Lindóia: SBBq, 2008. Não paginado. PABMB. Biblioteca(s): Embrapa Agricultura Digital. |
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7. | | 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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10. | | MAZONI, I.; BORRO, L. C.; JARDINE, J. G.; YANO, I. H.; SALIM, J. A.; NESHICH, G. Study of specific nanoenvironments containing α-helices in all-α and ([α]+[β])+([α]/[β]) proteins. Plos One, v. 13, n. 7, p. 1-25, 2018. Artigo e0200018. Biblioteca(s): Embrapa Agricultura Digital; Embrapa Territorial. |
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11. | | MAZONI, I.; BORRO, L. C.; ALVARENGA, D.; JARDINE, J. G.; NESHICH, G. Studying structure function relationship of proteins using "remediated" PDB files. In: ANNUAL MEETING OF SBBQ, 37.; CONGRESS OF THE PAN-AMERICAN ASSOCIATION FOR BIOCHEMISTRY AND MOLECULAR BIOLOGY, 11, 2008, Águas de Lindóia. Program and index... Águas de Lindóia, Program and index... Águas de Lindóia: SBBq, 2008. Não paginado. PABMB. Biblioteca(s): Embrapa Agricultura Digital. |
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13. | | 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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14. | | 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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15. | | 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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16. | | 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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17. | | FULAZ, S. F.; CABRINI, F. M.; CARVALHO, D. J. P.; BORRO, L. C.; SANTOS, C. A. dos; BELOTI, L. L.; NESHICH, G.; SOUZA, A. P. de; TASIC, L. Design of inhibitors for the PilT protein from Xylella fastidiosa using in silico and in vitro approaches. In: ANNUAL MEETING OF THE BRAZILIAN SOCIETY FOR BIOCHEMISTRY AND MOLECULAR BIOLOGY, 45., 2016, Natal. Livro de resumos... [Natal]: Sociedade Brasileira de Bioquímica e Biologia Molecular, 2016. Não paginado. Biblioteca(s): Embrapa Agricultura Digital. |
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18. | | 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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19. | | 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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20. | | YAMAGISHI, M. E. B.; FALCAO, P. R. K.; BORRO, L. C.; OLIVEIRA, S. R. de M.; SANTOS, E. H. dos; JARDINE, J. G.; VIEIRA, F. D.; MAZONI, I.; NARCISO, M. G.; NESHICH, G. Analysing protein-protein interface using JPIV. 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-14. Na publicação: Paula R. Kuser-Falcão, Stanley R. M. Oliveira, Edgard H. Santos. Biblioteca(s): Embrapa Agricultura Digital. |
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Registros recuperados : 26 | |
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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
Biblioteca(s): |
Embrapa Agricultura Digital. |
Data corrente: |
26/11/2009 |
Data da última atualização: |
15/01/2020 |
Tipo da produção científica: |
Resumo em Anais de Congresso |
Autoria: |
MAZONI, I.; BORRO, L. C.; MANCINI, A.; SALIM, J. A.; MORAES, F. R.; JARDINE, J. G.; NESHICH, I. P.; NESHICH, G. |
Afiliação: |
IVAN MAZONI, CNPTIA; L. C. BORRO, CNPTIA; ADAUTO LUIZ MANCINI, CNPTIA; JOSÉ AUGUSTO SALIM, Estagiário/CNPTIA; FABIO ROGERIO DE MORAES, Bolsista/CNPTIA; JOSE GILBERTO JARDINE, CNPTIA; IZABELLA PENA NESHICH, Estagiária/CNPTIA; GORAN NESHICH, CNPTIA. |
Título: |
Computational analysis of the secondary structure elements based on the physical chemical and geometrical descriptors and statistics data. |
Ano de publicação: |
2009 |
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. |
Páginas: |
Não paginado |
Idioma: |
Inglês |
Notas: |
X-Meeting 2009. |
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 |
Palavras-Chave: |
Análise computacional; Elementos de estrutura secundária; JSSD. |
Thesagro: |
Dados Estatísticos. |
Thesaurus NAL: |
Computer software. |
Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
Marc: |
LEADER 02508nam a2200277 a 4500 001 1576280 005 2020-01-15 008 2009 bl uuuu u00u1 u #d 100 1 $aMAZONI, I. 245 $aComputational analysis of the secondary structure elements based on the physical chemical and geometrical descriptors and statistics data.$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 paginado 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 $aComputer software 650 $aDados Estatísticos 653 $aAnálise computacional 653 $aElementos de estrutura secundária 653 $aJSSD 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. P. 700 1 $aNESHICH, G.
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