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Registro Completo |
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Biblioteca(s): |
Embrapa Agricultura Digital; Embrapa Territorial. |
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Data corrente: |
17/02/2016 |
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Data da última atualização: |
30/11/2020 |
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Autoria: |
SALIM, J. A.; BORRO, L.; MAZONI, I.; JARDINE, J. G.; NESHICH, G. |
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Afiliação: |
JOSÉ AUGUSTO SALIM, Computational Biology Research Group; LUIZ BORRO, Computational Biology Research Group; IVAN MAZONI, CNPTIA; JOSÉ GILBERTO JARDINE, CNPM; GORAN NESIC, CNPTIA. |
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Título: |
Multiple Structures Single Parameter (MSSP): analysis of a single protein nano environment descriptor characterizing a shared loci on structurally aligned proteins. |
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Ano de publicação: |
2016 |
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Fonte/Imprenta: |
Bioinformatics Advance, v. 32, n. 12, p. 1885-1887, June 2016. |
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DOI: |
https://doi.org/10.1093/bioinformatics/btw082 |
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Idioma: |
Inglês |
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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 |
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Palavras-Chave: |
Amino acid residues; Bioinformática. |
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Thesaurus Nal: |
Bioinformatics. |
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Categoria do assunto: |
-- |
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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.
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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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