In molecular biology, MobiDB[1][2][3] is a curated biological database designed to offer a centralized resource for annotations of intrinsic protein disorder. Protein disorder is a structural feature characterizing a large number of proteins with prominent members known as intrinsically unstructured (or disordered) proteins. The database features three levels of annotation: manually curated, indirect and predicted. By combining different data sources of protein disorder into a consensus annotation, MobiDB aims at giving the best possible picture of the "disorder landscape" of a given protein of interest.
MobiDB
Content
Description
MobiDB database of protein disorder and mobility annotations
Curated data for MobiDB is obtained from DisProt[4] database giving information and disorder annotation manually extracted from literature. In order to complement disorder annotation, MobiDB features additional annotations from external sources:
UniProt: Annotations from the UniProt database include organism, subcellular location, tissue specificity, function, relevant sites, relevant regions, post-translational modifications, and linear motifs.
Pfam: protein domain annotations are displayed in graphical form and are link-enabled, allowing the user to visit the corresponding Pfam page for further information.
PDB: Secondary structure is extracted from the PDB whenever available, and displayed in graphical form and in 3D.
STRING: Known interactors with evidence in "database" and "experimental" are displayed in a sortable table.
Indirect sources
PDB X-ray: When a crystallographic experiment is done to try and resolve a protein's structure, there are cases where the position of certain residues can not be accurately determined. One of the possible causes of this is that the residue is part of a flexible/disordered region. For this reason missing residues in PDB experiments are considered an indication of intrinsic disorder.
PDB NMR: Deposited files of NMR experiments for protein structure resolution often contain multiple models, representing different conformations of the same protein. By calculating the differences between the positions of each model's residues, one can measure the degree in which this positions change. This change can be interpreted as a measure of how flexible or disordered a protein is. The MOBI web server (from which the name of this database was derived) automates this calculations taking as input a PDB formatted file.
Predictions
A great variety of intrinsic protein disorder predictors have been trained in the last decade. The bulk of them are trained to mimic the nature of the annotations previously described. Since MobiDB currently covers the full set of UniProt sequences, the included predictors need to be extremely fast. Ten predictors currently included (ESpritz in its three flavours, IUPred in its two flavours, DisEMBL in two of its flavours, GlobPlot, VSL2b and JRONN) enable MobiDB to provide disorder annotations for every protein, even when no curated or indirect data is available.
MobiDB consensus
In order to provide the best possible annotation for a given protein, MobiDB combines all its data sources into a consensus annotation. This annotation differs from the ones belonging to the sources themselves in that it features a third state, in addition to "structured" and "disordered": when two authoritative sources disagree, it displays the region as "ambiguous". With the currently available annotations, this conflict arises when a manually curated source annotates a certain region as disordered, and yet there is a PDB structure available for that same region.
Website
MobiDB website provides users with an interface to search by UniProt ID, protein name or free text. Following the submission, users are presented with a list of proteins each one annotated with disorder information integrated from various sources including consensus disorder prediction.
MobiDB web-server exposes some RESTful endpoints allowing programmatic access to MobiDB and retrieval of different data types. Available GET routes provide access to UniProt, STRING, Pfam and disorder data in JSON format.
External links
MobiDB homepage
References
^Di Domenico, Tomás; Walsh, Ian; Martin, Alberto J. M.; Tosatto, Silvio C. E. (2012-08-01). "MobiDB: a comprehensive database of intrinsic protein disorder annotations". Bioinformatics. 28 (15): 2080–2081. doi:10.1093/bioinformatics/bts327. ISSN 1367-4811. PMID 22661649.
^Potenza, Emilio; Di Domenico, Tomás; Walsh, Ian; Tosatto, Silvio C. E. (2015-01-01). "MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins". Nucleic Acids Research. 43 (Database issue): D315–320. doi:10.1093/nar/gku982. ISSN 1362-4962. PMC4384034. PMID 25361972.
^Piovesan, Damiano; Tabaro, Francesco; Mičetić, Ivan; Necci, Marco; Quaglia, Federica; Oldfield, Christopher J.; Aspromonte, Maria Cristina; Davey, Norman E.; Davidović, Radoslav (2016-12-13). "DisProt 7.0: a major update of the database of disordered proteins". Nucleic Acids Research. 45 (D1): D1123–D1124. doi:10.1093/nar/gkw1279. ISSN 1362-4962. PMC5210598. PMID 27965415.
January 07, 2023
mobidb, molecular, biology, curated, biological, database, designed, offer, centralized, resource, annotations, intrinsic, protein, disorder, protein, disorder, structural, feature, characterizing, large, number, proteins, with, prominent, members, known, intr. In molecular biology MobiDB 1 2 3 is a curated biological database designed to offer a centralized resource for annotations of intrinsic protein disorder Protein disorder is a structural feature characterizing a large number of proteins with prominent members known as intrinsically unstructured or disordered proteins The database features three levels of annotation manually curated indirect and predicted By combining different data sources of protein disorder into a consensus annotation MobiDB aims at giving the best possible picture of the disorder landscape of a given protein of interest MobiDBContentDescriptionMobiDB database of protein disorder and mobility annotationsData typescapturedAnnotation of protein mobility and disorderOrganismsAllContactResearch centerDepartment of Biomedical Sciences at University of PaduaLaboratoryBioComputing UPPrimary citationPMID 29136219Release dateDecember 2017AccessData formatJSONWebsitemobidb orgWeb service URLREST API see info hereMiscellaneousLicenseCC BY 4 0Version3 0 0Curation policyYes manual and automatic Contents 1 MobiDB data sources 1 1 Curated data and additional annotation 1 2 Indirect sources 1 3 Predictions 2 MobiDB consensus 3 Website 4 External links 5 ReferencesMobiDB data sources EditCurated data and additional annotation Edit Curated data for MobiDB is obtained from DisProt 4 database giving information and disorder annotation manually extracted from literature In order to complement disorder annotation MobiDB features additional annotations from external sources UniProt Annotations from the UniProt database include organism subcellular location tissue specificity function relevant sites relevant regions post translational modifications and linear motifs Pfam protein domain annotations are displayed in graphical form and are link enabled allowing the user to visit the corresponding Pfam page for further information PDB Secondary structure is extracted from the PDB whenever available and displayed in graphical form and in 3D STRING Known interactors with evidence in database and experimental are displayed in a sortable table Indirect sources Edit PDB X ray When a crystallographic experiment is done to try and resolve a protein s structure there are cases where the position of certain residues can not be accurately determined One of the possible causes of this is that the residue is part of a flexible disordered region For this reason missing residues in PDB experiments are considered an indication of intrinsic disorder PDB NMR Deposited files of NMR experiments for protein structure resolution often contain multiple models representing different conformations of the same protein By calculating the differences between the positions of each model s residues one can measure the degree in which this positions change This change can be interpreted as a measure of how flexible or disordered a protein is The MOBI web server from which the name of this database was derived automates this calculations taking as input a PDB formatted file Predictions Edit A great variety of intrinsic protein disorder predictors have been trained in the last decade The bulk of them are trained to mimic the nature of the annotations previously described Since MobiDB currently covers the full set of UniProt sequences the included predictors need to be extremely fast Ten predictors currently included ESpritz in its three flavours IUPred in its two flavours DisEMBL in two of its flavours GlobPlot VSL2b and JRONN enable MobiDB to provide disorder annotations for every protein even when no curated or indirect data is available MobiDB consensus EditIn order to provide the best possible annotation for a given protein MobiDB combines all its data sources into a consensus annotation This annotation differs from the ones belonging to the sources themselves in that it features a third state in addition to structured and disordered when two authoritative sources disagree it displays the region as ambiguous With the currently available annotations this conflict arises when a manually curated source annotates a certain region as disordered and yet there is a PDB structure available for that same region Website EditMobiDB website provides users with an interface to search by UniProt ID protein name or free text Following the submission users are presented with a list of proteins each one annotated with disorder information integrated from various sources including consensus disorder prediction MobiDB web server exposes some RESTful endpoints allowing programmatic access to MobiDB and retrieval of different data types Available GET routes provide access to UniProt STRING Pfam and disorder data in JSON format External links EditMobiDB homepageReferences Edit Di Domenico Tomas Walsh Ian Martin Alberto J M Tosatto Silvio C E 2012 08 01 MobiDB a comprehensive database of intrinsic protein disorder annotations Bioinformatics 28 15 2080 2081 doi 10 1093 bioinformatics bts327 ISSN 1367 4811 PMID 22661649 Potenza Emilio Di Domenico Tomas Walsh Ian Tosatto Silvio C E 2015 01 01 MobiDB 2 0 an improved database of intrinsically disordered and mobile proteins Nucleic Acids Research 43 Database issue D315 320 doi 10 1093 nar gku982 ISSN 1362 4962 PMC 4384034 PMID 25361972 Piovesan Damiano Tabaro Francesco Paladin Lisanna Necci Marco Micetic Ivan Camilloni Carlo Davey Norman Dosztanyi Zsuzsanna Meszaros Balint 2018 01 04 MobiDB 3 0 more annotations for intrinsic disorder conformational diversity and interactions in proteins Nucleic Acids Research 46 D1 D471 D476 doi 10 1093 nar gkx1071 PMC 5753340 PMID 29136219 Piovesan Damiano Tabaro Francesco Micetic Ivan Necci Marco Quaglia Federica Oldfield Christopher J Aspromonte Maria Cristina Davey Norman E Davidovic Radoslav 2016 12 13 DisProt 7 0 a major update of the database of disordered proteins Nucleic Acids Research 45 D1 D1123 D1124 doi 10 1093 nar gkw1279 ISSN 1362 4962 PMC 5210598 PMID 27965415 Retrieved from https en wikipedia org w index php title MobiDB amp oldid 1070318495, wikipedia, wiki, book, books, library,
