MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins.
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.
Affiliation: Department of Biomedical Sciences, University of Padua, 35131 Padova, Italy.Show MeSH
Related in: MedlinePlus
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.
Affiliation: Department of Biomedical Sciences, University of Padua, 35131 Padova, Italy.