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Protocols

MobiDB specifications

Information


Unique identifier OMICS_04131
Name MobiDB
Restrictions to use None
Database management system PostgreSQL
Community driven No
Data access File download, Browse, Application programming interface
User data submission Not allowed
Version 3.0
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/MobiDB

Maintainer


  • person_outline Silvio Tosatto

Publications for MobiDB

MobiDB citations

 (18)
library_books

Functional and structural characterization of osteocytic MLO Y4 cell proteins encoded by genes differentially expressed in response to mechanical signals in vitro

2018
Sci Rep
PMCID: 5928037
PMID: 29712973
DOI: 10.1038/s41598-018-25113-4

[…] n observation that this results in a better predictive quality when compared to the use of individual predictors,. Such consensuses are also implemented in the current databases of putative disorder: MobiDB, and D2P2 , and were utilized in many other studies,,,,,,. We quantified amount of disorder with the disorder content, which is defined as a fraction of disordered amino acids in a given sequen […]

library_books

Structural disorder of plasmid encoded proteins in Bacteria and Archaea

2018
BMC Bioinformatics
PMCID: 5922023
PMID: 29699482
DOI: 10.1186/s12859-018-2158-6

[…] We could not use data from databases containing pre-calculated disorder level (such as [, ]) because of the small intersection of protein sets in our material and in these databases. For example, MobiDB includes only 5% of proteins from our dataset (comparison was done by using corresponding UniProt ids). The disorder level for each residue of each protein in our dataset was calculated using t […]

library_books

Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder Enriched Interactions

2017
Int J Mol Sci
PMCID: 5751360
PMID: 29257115
DOI: 10.3390/ijms18122761

[…] to the use of individual predictors [,]. The same consensus was utilized in a number of other studies [,,,,,,]. Similar, consensus-based putative annotations of disorder can be also obtained from the MobiDB [,] and D2P2 [] databases. In agreement with these works and conventions in this field of research [], we removed putative disordered segments with less than four consecutive residues. We quant […]

call_split

A Comprehensive Survey of the Roles of Highly Disordered Proteins in Type 2 Diabetes

2017
Int J Mol Sci
PMCID: 5666700
PMID: 28934129
DOI: 10.3390/ijms18102010
call_split See protocol

[…] disorder, such as native coils and native pre-molten globules [].To analyze the consensus intrinsic disorder and to find disorder-based interaction sites, molecular recognition features (MoRFs), the MobiDB database [,], the ANCHOR algorithm [,], and the MoRFchibi system [] were used. The MobiDB database combines different data sources related to protein disorder into a consensus annotation, and w […]

library_books

Potential Roles of Intrinsic Disorder in Maternal Effect Proteins Involved in the Maintenance of DNA Methylation

2017
Int J Mol Sci
PMCID: 5618547
PMID: 28869544
DOI: 10.3390/ijms18091898

[…] 120–142) is predicted to be ordered. C shows that human PGC7 is predicted to have several IDPRs (residues 1–61, 100–126 and 143–159).We further analysed the disorder status of PGC7 proteins using the MobiDB database (http://mobidb.bio.unipd.it/) [,], which provides consensus disorder scores by aggregating the output from 10 predictors. The consensus MobiDB CPDR values of mouse PGC7 (UniProt ID: Q8 […]

call_split

Novel interactions of the von Hippel Lindau (pVHL) tumor suppressor with the CDKN1 family of cell cycle inhibitors

2017
Sci Rep
PMCID: 5397843
PMID: 28425505
DOI: 10.1038/srep46562
call_split See protocol

[…] ) and p57 (P49918) were retrieved from UniProt selecting the canonical sequence and visualized with Jalview. Alignment was performed with T-Coffee using default parameters. Disorder was assessed with MobiDB and DisProt, while functional domains were retrieved from Pfam and InterPro. A protein-protein interaction network centered around pVHL and CDKNs was derived from STRING. To maximize data relia […]

Citations

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MobiDB institution(s)
Department of Biomedical Sciences, University of Padua, Padua, Italy; Institute of Biosciences and Medical Technology, Tampere, Finland; Department of Agricultural Sciences, University of Udine, Udine, Italy; Fondazione Edmund Mach, S. Michele all’Adige, Italy; Department of Biosciences, University of Milan, Milano, Italy; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin, Ireland; UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin, Ireland; MTA-ELTE Lendulet Bioinformatics Research Group, Department of Biochemistry, Budapest, Hungary; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary; Structural Bioinformatics Group, Department of Science and Technology, National University of Quilmes, CONICET, Bernal, Argentina; Department of Chemistry, University of Cambridge, Cambridge, UK; Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium; VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology (VIB), Brussels, Belgium; Interuniversity Institute of Bioinformatics in Brussels, ULB/VUB, Brussels, Belgium; CNR Institute of Neuroscience, Padua, Italy
MobiDB funding source(s)
Supported by COST Action [BM1405 NGP-net]; FIRC Research Fellowship [16621]; Hungarian Academy of Sciences ‘Lendulet’ Grant [LP201418/2016]; Hungarian Scientific Research Fund [OTKA K 108798]; Hungarian Academy of Sciences Postdoctoral Fellowship; Agencia de Ciencia y Tecnologia [PICT-2014–3430]; Universidad Nacional de Quilmes [1402/15]; OTKA Grant [PD-OTKA 108772]; Research Foundation Flanders (FWO) Odysseus Grant [G.0029.12]; FWO project [G032816N] and AIRC IG Grant [17753].

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