MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins

By Damiano Piovesan, Francesco Tabaro, L. Paladin, Marco Necci, I. Mičetić, Carlo Camilloni, Norman E. Davey, Zsuzsanna Dosztányi, Bálint Mészáros, Alexander Miguel Monzon and 7 more. 2017

194 citations recorded by the source corpus.

Abstract The MobiDB (URL: mobidb.bio.unipd.it) database of protein disorder and mobility annotations has been significantly updated and upgraded since its last major renewal in 2014. Several curated datasets for intrinsic disorder and folding upon binding have been integrated from specialized databases. The indirect evidence has also been expanded to better capture information available in the PDB, such as high temperature residues in X-ray structures and overall conformational diversity. Novel nuclear magnetic resonance chemical shift data provides an additional experimental information layer on conformational dynamics. Predictions have been expanded to provide new types of annotation on backbone rigidity, secondary structure preference and disordered binding regions. MobiDB 3.0 contains information for the complete UniProt protein set and synchronization has been improved by covering all UniParc sequences. An advanced search function allows the creation of a wide array of custom-made datasets for download and further analysis. A large amount of information and cross-links to more specialized databases are intended to make MobiDB the central resource for the scientific community working on protein intrinsic disorder and mobility.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding (2018, background): “However, integration into several resources, such as MobiDBlite (41), MobiDB 3.0 (42) and InterPro (43) made it necessary to implement several minor bug-fixes.”
InterPro in 2019: improving coverage, classification and access to protein sequence annotations (2018, methodology): “…about sequence features, such as consensus annotation of long-range intrinsic disorder (provided by MobiDB-lite, a derivative of the MobiDB database (15)) and prediction of signal peptides, transmembrane regions and coiled-coils, via the SignalP, Phobius, TMHMM and Coils software packages (16–19).”
The InterPro protein families and domains database: 20 years on (2020, background): “InterPro also offers additional annotations on sequence features such as intrinsic protein disorder regions (provided by MobiDB-lite, part of the MobiDB database (13)), and signal peptides, transmembrane regions and coiled-coils (provided by Coils (14), Phobius (15), SignalP (16) and TMHMM (17)).”
Pfam: The protein families database in 2021 (2020, methodology): “For each family we determined the fraction of residues in the seed alignment that were predicted to be low complexity by segmasker (24) or disordered by MobiDB-lite (25).”