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

By Emilio Potenza, Tomás Di Domenico, Ian Walsh, Silvio C. E. Tosatto. 2014

190 citations recorded by the source corpus.

MobiDB (http://mobidb.bio.unipd.it/) is a database of intrinsically disordered and mobile proteins. Intrinsically disordered regions are key for the function of numerous proteins. Here we provide a new version of MobiDB, a centralized source aimed at providing the most complete picture on different flavors of disorder in protein structures covering all UniProt sequences (currently over 80 million). The database features three levels of annotation: manually curated, indirect and predicted. Manually curated data is extracted from the DisProt database. Indirect data is inferred from PDB structures that are considered an indication of intrinsic disorder. The 10 predictors currently included (three ESpritz flavors, two IUPred flavors, two DisEMBL flavors, GlobPlot, VSL2b and JRONN) enable MobiDB to provide disorder annotations for every protein in absence of more reliable data. The new version also features a consensus annotation and classification for long disordered regions. In order to complement the disorder annotations, MobiDB features additional annotations from external sources. 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.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning (2019, methodology): “These datasets were the subsets from the established SL477 [16], MobiDB [43], and DisProt Complement [44] sets, respectively, after removing long proteins (>700 residues) and homologous proteins in our training dataset (25% sequence identity cutoff with BLASTClust).”
The Pfam protein families database: towards a more sustainable future (2015, positive): “In collaboration with the authors of the MobiDB resource (15), we have identified regions longer than 100 residues in primate proteins that appear conserved and have used them as primers to build new Pfam entries.”
InterPro in 2017—beyond protein family and domain annotations (2016, methodology): “Integration of MobiDB Lite annotation within InterPro, enabling annotation of intrinsic disordered (ID) regions within proteins.”
DisProt 7.0: a major update of the database of disordered proteins (2016, neutral): “…(15), Mo-biDB, which features three levels of annotations, manually curated, indirect and predicted for all UniProt sequences (over 80 million) (16), and IDEAL, which contains manual annotations of interaction regions undergoing induced folding, sites of post-translational modifications and…”
The RING 2.0 web server for high quality residue interaction networks (2016, background): “It is an intrinsically disordered protein (38) lacking a hydrophobic core characterized by consecutive secondary structure elements not interacting with each other.”
How Common Is Disorder? Occurrence of Disordered Residues in Four Domains of Life (2015, methodology): “To this end, several databases are currently available: PROSITE, InterPro, Pfam, and ModiDP [1–4].”
Disorder Prediction Methods, Their Applicability to Different Protein Targets and Their Usefulness for Guiding Experimental Studies (2015, methodology): “An example of such a database is the MobiDB, which contains disordered proteins sourced from the PDB and DisProt, exploiting multiple disorder prediction methods [37].”
ProViz—a web-based visualization tool to investigate the functional and evolutionary features of protein sequences (2016, background): “Sequence analysis tools can accurately define regions of proteins that are unlikely to have any structure in their native state (20,21) and predict protein membrane topology relative to membrane crossing regions (22).”
FuzDB: database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies (2016, background): “The functional information of MobiDB (16) is imported from other databases and does not focus on the ID region(s).”
Sequence Determinants of Intracellular Phase Separation by Complex Coacervation of a Disordered Protein (2016, methodology): “0 (Potenza et al., 2015) to identify long (>100 residue) IDRs with sequence properties similar to NICD.”