How to use
Basics
The main aim of IUPred2 is to identify Intrinsically Disordered Protein Regions (IDPRs, i.e.
regions that lack a stable monomeric structure under native
conditions) based on a biophysics-based model.
The user can input any protein sequence and IUPred returns a score between 0 and 1 for each
residue, corresponding to the probability of the given
residue being part of a disordered region.
The disordered nature of a protein segment can be context dependent: certain protein regions
can switch between an ordered and a disordered state
depending on various environmental factors. Currently, the IUPred2A server is able to detect
such context-dependent disorder in the case where the
environmental factors are either a change in the redox state or the presence of an ordered
binding partner (for more details see
here).
The following sections outline the use of IUPred2A in various scenarios. For a list of
select example runs highlighting various IUPred2A features,
see the Examples section.
Protein sequence input
There are three basic ways to input protein sequences into IUPred2A:
I - If the protein is deposited in the UniProt database (either in SwissProt or
TrEMBL) you can specify the accession
code or the ID of the protein in the "Enter SWISS-PROT/TrEMBL identifier or accession
number" field. The IUPred2A server
is always linked to newest version of UniProt. The header of the UniProt entry will be
displayed as the title in the results page.
II - Type or cut and paste your sequence in the "paste the amino acid sequence"
field.
The amino acid sequence must be in the standard FASTA
format or must be a plain sequence.
Spaces and other non-standard
characters within the pasted sequence are permitted, however they will be removed with the
remaining sequence treated as a single
continuous chain.
III - For analysis of a large number of sequences/full proteomes, users can upload
their sequences in a single file adhering to
the standard multiple FASTA file format criteria. In this case the output will be provided
in text format via email.
Prediction type
There are three different disorder prediction types offered, each using different parameters
optimized for slightly different applications.
These are: long disorder, short disorder, and structured domains.
Long disorder (default option):
The main profile of IUPred2A is to predict global structural disorder that encompasses at
least 30 consecutive residues of the protein. The
long option is optimized for this task.
Short disorder:
In this setting, IUPred2A uses a parameter set best suited for predicting short disordered
regions, such as missing residues in the X-ray
structure of an otherwise globular protein. For this application a smaller sequential
neighbourhood of residues is considered for the
calculation of the IUPred score. As chain termini of globular proteins are often disordered
in X-ray structures, this is taken into account
by an end-adjustment parameter which favors disorder prediction at the ends.
Structured domains:
The reliable identification of ordered protein regions is a crucial step in target selection
for structural studies and structural genomics
projects. Finding putative structured domains suitable for structure determination is
another potential application of IUPred2A. In this
case the algorithm aims to find continuous regions confidently predicted ordered.
Neighbouring regions close to each other are merged,
while regions shorter than the minimal domain size of at least 30 residues are ignored. When
this prediction type is selected, the region(s)
predicted to correspond to structured/globular domains are returned.
Context-dependent predictions
IDPRs often harbor binding regions that are able to specifically interact with a globular
domain. During this interaction, in the majority
of known cases, the binding disordered region adopts an ordered structure in its bound form.
This is probably the most commonly occurring
context-dependent protein disorder, where the transition between the unstructured and the
structured states is initiated by the presence of
an appropriate protein partner. Such disordered binding regions are identified using the
ANCHOR2 prediction algorithm. Similarly to IUPred2, ANCHOR2
also assigns to each residue a score between 0 and 1, representing the probability of the
given residue to be part of a disordered binding region.
Selecting ANCHOR2 as a prediction option, the ANCHOR2 score is provided along with the
IUPred
score.
Another known context-dependent behaviour of IDPRs is the change between a folded and an
unfolded state as a result of a change in the redox state. Such protein regions can be
ordered or disordered depending on their localization in/outside the cell. Upon selecting
this option, IUPred2A marks such redox-sensitive protein regions, and also shows their
maximal and minimal predicted disorder tendencies.
Output
Basic features:
The primary output of IUPred2A is a graph showing the disorder tendency of each residue in
the given protein, where higher values correspond
to a higher probability of disorder. The graph is scalable and can be directly downloaded
for presentation/publication purposes. The list of
position-specific disorder scores is also downloadable in simple text or JSON
format.
Extended features:
If the prediction was run by specifying a UniProt ID/accession, the output of IUPred2A also
shows additional protein annotations, including
Pfam regions; post-translational
modifications (PTMs), including phosphorylations (upper line),
methylations and acetylations (lower line) taken from PhosphoSitePlus;
corresponding structures
from the PDB; and regions that were
experimentally verified to be disordered, taken from
DisProt, DIBS, and
MFIB.
If context-dependent predictions were selected, the output graph and the downloadable
results incorporate additional data as well.
In case of disordered binding region prediction via ANCHOR2, the graph shows the probability
of each residue being part of a binding region in blue.
The presence or absence of the IUPred2 and ANCHOR2 scores are switchable by clicking on the
legend.
If redox state-dependent predictions were enabled, the ranges of possible disorder
tendencies for redox- sensitive regions of the query protein are marked in purple.
REST API
IUPred2A is also accessible via REST API to enable automated/large scale use. Requests
should be input following the syntax:
http://iupred2a.elte.hu/iupred2a/::accession::
or
http://iupred2a.elte.hu/iupred2a/::iupred_type::/::accession::
In case ::iupred_type:: is not given, the default "long" will be used.
If the requested URL ends with ".json" the output
will be JSON type, in any other case it will be simple text.
Examples:
http://iupred2a.elte.hu/iupred2a/q32p44
http://iupred2a.elte.hu/iupred2a/q32p44.json
http://iupred2a.elte.hu/iupred2a/short/q32p44
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