DisProt

DisProt is a manually curated biological database of

intrinsically disordered proteins (IDPs) and regions
DisProt
(IDRs).[1][2][3] DisProt annotations cover state
information on the protein but also, when available, its
state transitions, interactions and functional aspects of
disorder detected by specific experimental methods.
Content
DisProt is hosted and maintained in the BioComputing
UP laboratory (Dept. of Biomedical Sciences, Description Manually curated database
University of Padua). of Intrinsically Disordered
Proteins (IDPs) and regions
Website (IDRs)
Data types Intrinsically Disordered
The latest DisProt version, DisProt 9,[3] includes more captured Proteins
than 2300 protein entries and more than 4500 pieces of Organisms all
evidence of structural state, state transitions, interactions
and functions, along with more than 2500 scientific Contact
publications annotated. Laboratory BioComputing UP
laboratory (Dept. of
Biomedical Sciences,
Biocuration in DisProt
University of Padova)
DisProt entries are annotated by professional and Primary citation PMID 34850135 (https://pu
community biocurators from experimental data bmed.ncbi.nlm.nih.gov/348
published in scientific literature. The DisProt home page 50135)
features examples of DisProt entries, i.e. p53 and
Access
Catenin beta-1, along with entries of proteins belonging
to the SARS-CoV-2 virus, e.g. Nucleoprotein. Website https://disprot.org/
Download URL https://disprot.org/download
Thematic datasets Miscellaneous
License Creative Commons
Starting 2020, DisProt releases ‘thematic datasets’
Attribution 4.0 International
describing biological areas where IDPs are involved in
(CC BY 4.0) License
and play a crucial role.[3] All the entries belonging to
these datasets are tagged with the name of the theme. Curation policy Manual curation from
professional and
Unicellular toxins and antitoxins (DisProt community biocurators
release 2020_12)
Extracellular matrix proteins (DisProt release 2021_06)
Viral proteins (DisProt release 2021_12)

Model organism entries

 In the DisProt home
page model
organisms are
represented by an
icon, the name of the
species and the
number of DisProt
entries belonging to
each specific
organism. Entries
from the following
organisms are
accessible from the
DisProt home page
under the
‘Organisms’ section
and can be
downloaded as
single files: Homo
sapiens, Mus
musculus, Rattus
norvegicus,
Saccharomices
cerevisiae,
DisProt 9
Escherichia coli,
Arabidopsis
thaliana, Drosophila
melanogaster, Caenorhabditis elegans.

DisProt versions and releases

DisProt versions and releases include changes to the website and to the manually curated content of the
database.

DisProt 7[4] (2016): more than 800 protein entries and 1000 publications annotated. Each
protein entry in DisProt is characterized by a DisProt identifier which takes the form of the
prefix DP followed by a 5 digit protein identifier, e.g. DP00016 corresponds to the Cyclin-
dependent kinase inhibitor 1 protein. It featured a new web interface based on Angular.JS.
DisProt 8[5] (2019): more than 1400 protein entries and over 3000 disordered protein
regions. DisProt 8 also introduced the concept of a stable DisProt region identifier. DisProt
has been widely used to train machine learning (ML) methods to predict disordered regions
in proteins. In addition, DisProt has been used to understand the properties of intrinsically
unstructured proteins.[6] DisProt 8 featured a new web interface and an extended API and a
new annotation interface integrating text mining technologies.
DisProt 9[3] (2021): more than 2300 protein entries and more than 4500 pieces of evidence,
annotated from over 2500 scientific articles. DisProt 9 features a restyled web interface and
a refactored Intrinsically Disordered Proteins Ontology (IDPO). Better interoperability is
provided through the adoption of the Gene Ontology (annotations of interactions and
 functions of IDPs and IDRs) and the Evidence and Conclusion Ontology (annotations of
experimental methods).

DisProt ontologies

DisProt uses three different ontologies to annotate disordered regions, the Intrinsically Disordered Proteins
Ontology (IDPO), the Evidence and Conclusion Ontology (ECO) and the Gene Ontology (GO). DisProt
has a dedicated page for each IDPO term that include the identifier, name and definition of the term
and cross-references to external ontologies, e.g. Gene Ontology. Each IDPO term page list all the DisProt
entries annotated with that specific term.

Intrinsically Disordered Proteins Ontology: used to annotate the following types of evidence,
1. structural state (i.e. disorder, pre-molten globule, molten globule, order), 2. structural
transition (transitions between structural states), and 3. self-functions (e.g. self-inhibition)
and functions associated with the unstructured state of the protein (e.g. flexible linker/spacer)
Evidence and Conclusion Ontology: used to annotate the experimental methods used to
assess the presence of intrinsic disorder or one of its aspects, e.g. circular dichroism
evidence.
Gene Ontology: used to annotate binding partners, e.g. protein binding, and other functions,
e.g. RNA folding chaperone.

External links
DisProt homepage (http://www.disprot.org)
DisProt blog (https://biocomputingup.github.io/disprot/)

References
1. Vucetic, Slobodan; Obradovic, Zoran; Vacic, Vladimir; Radivojac, Predrag; Peng, Kang;
Iakoucheva, Lilia M.; Cortese, Marc S.; Lawson, J. David; Brown, Celeste J. (2005-01-01).
"DisProt: a database of protein disorder" (https://doi.org/10.1093%2Fbioinformatics%2Fbth4
76). Bioinformatics. 21 (1): 137–140. doi:10.1093/bioinformatics/bth476 (https://doi.org/10.10
93%2Fbioinformatics%2Fbth476). ISSN 1367-4803 (https://www.worldcat.org/issn/1367-480
3). PMID 15310560 (https://pubmed.ncbi.nlm.nih.gov/15310560).
2. Sickmeier, Megan; Hamilton, Justin A.; LeGall, Tanguy; Vacic, Vladimir; Cortese, Marc S.;
Tantos, Agnes; Szabo, Beata; Tompa, Peter; Chen, Jake (2007-01-01). "DisProt: the
Database of Disordered Proteins" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1751543).
Nucleic Acids Research. 35 (Database issue): D786–793. doi:10.1093/nar/gkl893 (https://do
i.org/10.1093%2Fnar%2Fgkl893). ISSN 1362-4962 (https://www.worldcat.org/issn/1362-496
2). PMC 1751543 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1751543).
PMID 17145717 (https://pubmed.ncbi.nlm.nih.gov/17145717).
3. Quaglia, Federica; Mészáros, Bálint; Salladini, Edoardo; Hatos, András; Pancsa, Rita;
Chemes, Lucía B.; Pajkos, Mátyás; Lazar, Tamas; Peña-Díaz, Samuel; Santos, Jaime; Ács,
Veronika (2021-11-25). "DisProt in 2022: improved quality and accessibility of protein
intrinsic disorder annotation" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728214).
Nucleic Acids Research. 50 (D1): D480–D487. doi:10.1093/nar/gkab1082 (https://doi.org/10.
1093%2Fnar%2Fgkab1082). ISSN 1362-4962 (https://www.worldcat.org/issn/1362-4962).
PMC 8728214 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728214). PMID 34850135
(https://pubmed.ncbi.nlm.nih.gov/34850135).
 4. Piovesan, Damiano; Tabaro, Francesco; Mičetić, Ivan; Necci, Marco; Quaglia, Federica;
Oldfield, Christopher J.; Aspromonte, Maria Cristina; Davey, Norman E.; Davidović,
Radoslav (2016-11-28). "DisProt 7.0: a major update of the database of disordered proteins"
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210544). Nucleic Acids Research. 45 (D1):
D219–D227. doi:10.1093/nar/gkw1056 (https://doi.org/10.1093%2Fnar%2Fgkw1056).
ISSN 1362-4962 (https://www.worldcat.org/issn/1362-4962). PMC 5210544 (https://www.ncb
i.nlm.nih.gov/pmc/articles/PMC5210544). PMID 27899601 (https://pubmed.ncbi.nlm.nih.gov/
27899601).
5. Hatos, András; Hajdu-Soltész, Borbála; Monzon, Alexander M.; Palopoli, Nicolas; Álvarez,
Lucía; Aykac-Fas, Burcu; Bassot, Claudio; Benítez, Guillermo I.; Bevilacqua, Martina;
Chasapi, Anastasia; Chemes, Lucia (2019). "DisProt: intrinsic protein disorder annotation in
2020" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145575). Nucleic Acids Research.
48 (D1): D269–D276. doi:10.1093/nar/gkz975 (https://doi.org/10.1093%2Fnar%2Fgkz975).
PMC 7145575 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145575). PMID 31713636
(https://pubmed.ncbi.nlm.nih.gov/31713636).
6. Kovačević JJ (June 2012). "Computational analysis of position-dependent disorder content
in DisProt database" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5056116). Genomics
Proteomics Bioinformatics. 10 (3): 158–65. doi:10.1016/j.gpb.2012.01.002 (https://doi.org/10.
1016%2Fj.gpb.2012.01.002). PMC 5056116 (https://www.ncbi.nlm.nih.gov/pmc/articles/PM
C5056116). PMID 22917189 (https://pubmed.ncbi.nlm.nih.gov/22917189).

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