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MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins.

Potenza E, Di Domenico T, Walsh I, Tosatto SC - Nucleic Acids Res. (2014)

Bottom Line: Annotations from the UniProt database include post-translational modifications and linear motifs.Pfam annotations are displayed in graphical form and are link-enabled, allowing the user to visit the corresponding Pfam page for further information.Experimental protein-protein interactions from STRING are also classified for disorder content.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Sciences, University of Padua, 35131 Padova, Italy.

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Related in: MedlinePlus

Sequence annotations for alpha-synuclein (UniProt entry: P37840). (a) Overview disorder annotations combining DisProt, NMR, x-ray and predictors are shown. The highlighted red circle shows the experimentally determined and predicted long disordered region. Other information includes secondary structure and Pfam domains. Each of these annotations can be downloaded by clicking on the corresponding green button on the top right side of the page. (b) Detailed disorder annotation showing experimental (DisProt, NMR and x-ray) and predicted disorder (10 predictors). For each entry, it is possible to view the detailed sequence annotation by clicking on the green magnifying glass icon (see red circle and left inset). Where available, the 3D structure can be visualized to inspect interesting protein regions (see red circle and right inset). The red circle highlights the only known complete structure alpha-synuclein structure (PDB entry 2kkw). (c) Known protein–protein interactions deduced from PDB files and STRING are shown in analogy to the search results page, with color-coded long disorder percentage, length, protein name and organism. (d) Functional sequence features from UniProt, including binding sites, post-translational modifications and sequence regions.
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Figure 2: Sequence annotations for alpha-synuclein (UniProt entry: P37840). (a) Overview disorder annotations combining DisProt, NMR, x-ray and predictors are shown. The highlighted red circle shows the experimentally determined and predicted long disordered region. Other information includes secondary structure and Pfam domains. Each of these annotations can be downloaded by clicking on the corresponding green button on the top right side of the page. (b) Detailed disorder annotation showing experimental (DisProt, NMR and x-ray) and predicted disorder (10 predictors). For each entry, it is possible to view the detailed sequence annotation by clicking on the green magnifying glass icon (see red circle and left inset). Where available, the 3D structure can be visualized to inspect interesting protein regions (see red circle and right inset). The red circle highlights the only known complete structure alpha-synuclein structure (PDB entry 2kkw). (c) Known protein–protein interactions deduced from PDB files and STRING are shown in analogy to the search results page, with color-coded long disorder percentage, length, protein name and organism. (d) Functional sequence features from UniProt, including binding sites, post-translational modifications and sequence regions.

Mentions: The sequence visualization interface is shown in Figure 2 for alpha-synuclein, a protein involved in neurodegenerative disorders which is not yet well understood. The page is composed of a variety of boxes and sections that can be collapsed to optimize usage of the available workspace. Starting from the top right corner (Figure 2a), five download buttons are available for retrieving disordered row data and the other related annotations. In the ‘Protein overview’ box the user can find a basic description of the sequence, like Uniprot ID, protein name, organisms and so on. The main annotations located inside ‘Sequence annotations’ (Figure 2a), are displayed as bars by combining the original data sources. By clicking on the green magnifying glass button next to each annotation, it is possible to open a more detailed sequence viewer. The bars titled Disorder Sources, DisProt, PDB-NMR and PDB-xray are defined in the section ‘Combining experimental data’. While the prediction bars Predictors and Long Disorder are defined in ‘Disorder Predictors’ and ‘Long Disorder and Classification’ sections respectively. Other bars give a more comprehensive picture of the protein, displaying Pfam and secondary structure annotations. More detail is also shown on the visualization page. Figure 2b shows the detailed overview of the raw data, i.e. Disport, PDB-NMR, PDB-xray and Predictors in the section ‘Detailed disorder annotations’. Where a PDB is available, the user can visualize the protein structure in 3D, chain by chain or in the entire complex. Scrolling down the page, known interacting proteins from the PDB and STRING are classified by disorder content (see Figure 2c). Last but not least, relevant functional features provided by UniProt, such as post-translational modifications, binding site residues and low complexity regions, can be found at the bottom of the page (see Figure 2d). For a complete summary of MobiDB 2.0 improvements over the previous version see Supplementary Table S1. All the different annotations contribute towards a comprehensive molecular story about each UniProt entry.


MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins.

Potenza E, Di Domenico T, Walsh I, Tosatto SC - Nucleic Acids Res. (2014)

Sequence annotations for alpha-synuclein (UniProt entry: P37840). (a) Overview disorder annotations combining DisProt, NMR, x-ray and predictors are shown. The highlighted red circle shows the experimentally determined and predicted long disordered region. Other information includes secondary structure and Pfam domains. Each of these annotations can be downloaded by clicking on the corresponding green button on the top right side of the page. (b) Detailed disorder annotation showing experimental (DisProt, NMR and x-ray) and predicted disorder (10 predictors). For each entry, it is possible to view the detailed sequence annotation by clicking on the green magnifying glass icon (see red circle and left inset). Where available, the 3D structure can be visualized to inspect interesting protein regions (see red circle and right inset). The red circle highlights the only known complete structure alpha-synuclein structure (PDB entry 2kkw). (c) Known protein–protein interactions deduced from PDB files and STRING are shown in analogy to the search results page, with color-coded long disorder percentage, length, protein name and organism. (d) Functional sequence features from UniProt, including binding sites, post-translational modifications and sequence regions.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384034&req=5

Figure 2: Sequence annotations for alpha-synuclein (UniProt entry: P37840). (a) Overview disorder annotations combining DisProt, NMR, x-ray and predictors are shown. The highlighted red circle shows the experimentally determined and predicted long disordered region. Other information includes secondary structure and Pfam domains. Each of these annotations can be downloaded by clicking on the corresponding green button on the top right side of the page. (b) Detailed disorder annotation showing experimental (DisProt, NMR and x-ray) and predicted disorder (10 predictors). For each entry, it is possible to view the detailed sequence annotation by clicking on the green magnifying glass icon (see red circle and left inset). Where available, the 3D structure can be visualized to inspect interesting protein regions (see red circle and right inset). The red circle highlights the only known complete structure alpha-synuclein structure (PDB entry 2kkw). (c) Known protein–protein interactions deduced from PDB files and STRING are shown in analogy to the search results page, with color-coded long disorder percentage, length, protein name and organism. (d) Functional sequence features from UniProt, including binding sites, post-translational modifications and sequence regions.
Mentions: The sequence visualization interface is shown in Figure 2 for alpha-synuclein, a protein involved in neurodegenerative disorders which is not yet well understood. The page is composed of a variety of boxes and sections that can be collapsed to optimize usage of the available workspace. Starting from the top right corner (Figure 2a), five download buttons are available for retrieving disordered row data and the other related annotations. In the ‘Protein overview’ box the user can find a basic description of the sequence, like Uniprot ID, protein name, organisms and so on. The main annotations located inside ‘Sequence annotations’ (Figure 2a), are displayed as bars by combining the original data sources. By clicking on the green magnifying glass button next to each annotation, it is possible to open a more detailed sequence viewer. The bars titled Disorder Sources, DisProt, PDB-NMR and PDB-xray are defined in the section ‘Combining experimental data’. While the prediction bars Predictors and Long Disorder are defined in ‘Disorder Predictors’ and ‘Long Disorder and Classification’ sections respectively. Other bars give a more comprehensive picture of the protein, displaying Pfam and secondary structure annotations. More detail is also shown on the visualization page. Figure 2b shows the detailed overview of the raw data, i.e. Disport, PDB-NMR, PDB-xray and Predictors in the section ‘Detailed disorder annotations’. Where a PDB is available, the user can visualize the protein structure in 3D, chain by chain or in the entire complex. Scrolling down the page, known interacting proteins from the PDB and STRING are classified by disorder content (see Figure 2c). Last but not least, relevant functional features provided by UniProt, such as post-translational modifications, binding site residues and low complexity regions, can be found at the bottom of the page (see Figure 2d). For a complete summary of MobiDB 2.0 improvements over the previous version see Supplementary Table S1. All the different annotations contribute towards a comprehensive molecular story about each UniProt entry.

Bottom Line: Annotations from the UniProt database include post-translational modifications and linear motifs.Pfam annotations are displayed in graphical form and are link-enabled, allowing the user to visit the corresponding Pfam page for further information.Experimental protein-protein interactions from STRING are also classified for disorder content.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Sciences, University of Padua, 35131 Padova, Italy.

Show MeSH
Related in: MedlinePlus