| |
|
|
| 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. |
|    |
| 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. |
|  |
| 6. | | 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. |
| |
| 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. |
| |
| 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. |
| |
| 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. |
| |
| 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. |
| |
| 13. | | 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. |
| |
| 14. | | 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. |
| |
| 15. | | 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. |
| |
| 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. |
| |
| 17. | | 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. |
| |
| 18. | | 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. |
| |
| 19. | | 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. |
| |
| 20. | | 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. |
| |
| Registros recuperados : 34 | |
|
|
|
 | 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; Embrapa Territorial. |
|
Data corrente: |
17/02/2016 |
|
Data da última atualização: |
30/11/2020 |
|
Autoria: |
SALIM, J. A.; BORRO, L.; MAZONI, I.; JARDINE, J. G.; NESHICH, G. |
|
Afiliação: |
JOSÉ AUGUSTO SALIM, Computational Biology Research Group; LUIZ BORRO, Computational Biology Research Group; IVAN MAZONI, CNPTIA; JOSÉ GILBERTO JARDINE, CNPM; GORAN NESIC, CNPTIA. |
|
Título: |
Multiple Structures Single Parameter (MSSP): analysis of a single protein nano environment descriptor characterizing a shared loci on structurally aligned proteins. |
|
Ano de publicação: |
2016 |
|
Fonte/Imprenta: |
Bioinformatics Advance, v. 32, n. 12, p. 1885-1887, June 2016. |
|
DOI: |
https://doi.org/10.1093/bioinformatics/btw082 |
|
Idioma: |
Inglês |
|
Conteúdo: |
Motivation: A graphical representation of physicochemical and structural descriptors attributed to amino acid residues occupying the same topological position in different, structurally aligned proteins can provide a more intuitive way to associate possible functional implications to identified variations in structural characteristics. This could be achieved by observing selected characteristics of amino acids and of their corresponding nano environments, described by the numerical value of matching descriptor. For this purpose, a webbased tool called Multiple Structures Single Parameter (MSSP) was developed and here presented. Results: MSSP produces a 2D plot of a single protein descriptor for a number of structurally aligned protein chains. From a total of 150 protein descriptors available in MSSP, selected out of more than 1500 parameters stored in the STING database, it is possible to create easily readable and highly informative XY-plots, where X-axis contains the amino acid position in the multiple structural alignment, and Yaxis contains the descriptor?s numerical values for each aligned structure. To illustrate one of possible MSSP contributions to the investigation of changes in physicochemical and structural properties of mutants, comparing them to the cognate wild type structure, the oncogenic mutation of M918T in RET Kinase is presented. The comparative analysis of wild type and mutant structures shows great changes in their electrostatic potential. These variations are easily depicted at the MSSP generated XY plot. MenosMotivation: A graphical representation of physicochemical and structural descriptors attributed to amino acid residues occupying the same topological position in different, structurally aligned proteins can provide a more intuitive way to associate possible functional implications to identified variations in structural characteristics. This could be achieved by observing selected characteristics of amino acids and of their corresponding nano environments, described by the numerical value of matching descriptor. For this purpose, a webbased tool called Multiple Structures Single Parameter (MSSP) was developed and here presented. Results: MSSP produces a 2D plot of a single protein descriptor for a number of structurally aligned protein chains. From a total of 150 protein descriptors available in MSSP, selected out of more than 1500 parameters stored in the STING database, it is possible to create easily readable and highly informative XY-plots, where X-axis contains the amino acid position in the multiple structural alignment, and Yaxis contains the descriptor?s numerical values for each aligned structure. To illustrate one of possible MSSP contributions to the investigation of changes in physicochemical and structural properties of mutants, comparing them to the cognate wild type structure, the oncogenic mutation of M918T in RET Kinase is presented. The comparative analysis of wild type and mutant structures shows great changes in their electrostatic potential. These variati... Mostrar Tudo |
|
Palavras-Chave: |
Amino acid residues; Bioinformática. |
|
Thesaurus NAL: |
Bioinformatics. |
|
Categoria do assunto: |
-- |
|
Marc: |
LEADER 02303naa a2200217 a 4500
001 2127278
005 2020-11-30
008 2016 bl uuuu u00u1 u #d
024 7 $ahttps://doi.org/10.1093/bioinformatics/btw082$2DOI
100 1 $aSALIM, J. A.
245 $aMultiple Structures Single Parameter (MSSP)$banalysis of a single protein nano environment descriptor characterizing a shared loci on structurally aligned proteins.$h[electronic resource]
260 $c2016
520 $aMotivation: A graphical representation of physicochemical and structural descriptors attributed to amino acid residues occupying the same topological position in different, structurally aligned proteins can provide a more intuitive way to associate possible functional implications to identified variations in structural characteristics. This could be achieved by observing selected characteristics of amino acids and of their corresponding nano environments, described by the numerical value of matching descriptor. For this purpose, a webbased tool called Multiple Structures Single Parameter (MSSP) was developed and here presented. Results: MSSP produces a 2D plot of a single protein descriptor for a number of structurally aligned protein chains. From a total of 150 protein descriptors available in MSSP, selected out of more than 1500 parameters stored in the STING database, it is possible to create easily readable and highly informative XY-plots, where X-axis contains the amino acid position in the multiple structural alignment, and Yaxis contains the descriptor?s numerical values for each aligned structure. To illustrate one of possible MSSP contributions to the investigation of changes in physicochemical and structural properties of mutants, comparing them to the cognate wild type structure, the oncogenic mutation of M918T in RET Kinase is presented. The comparative analysis of wild type and mutant structures shows great changes in their electrostatic potential. These variations are easily depicted at the MSSP generated XY plot.
650 $aBioinformatics
653 $aAmino acid residues
653 $aBioinformática
700 1 $aBORRO, L.
700 1 $aMAZONI, I.
700 1 $aJARDINE, J. G.
700 1 $aNESHICH, G.
773 $tBioinformatics Advance$gv. 32, n. 12, p. 1885-1887, June 2016.
Download
Esconder MarcMostrar Marc Completo |
|
Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
|
|
Biblioteca |
ID |
Origem |
Tipo/Formato |
Classificação |
Cutter |
Registro |
Volume |
Status |
Fechar
|
| Nenhum registro encontrado para a expressão de busca informada. |
|
|
