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Getting started

Enter peptides
Load peptides by typing or from a file or choose a motif from the ELM data base
Modify the PSSM
Change the scoring methods and/or background distribution, and click on the heatmap to force or hide residues
Choose a species
The motif will be searched against the proteome of this species
Change the default options
For advanced users further options are available
Submit a new job
You will be redirected to the queue system during the search.
Further analyses
Once motifs are found you can launch a conservation or functional analysis, filter the instances, and visualize each instance.

Input

Use set of aligned peptides as input. The peptides must be aligned (i.e. has the same length) and can not contains non-standard amino acids. The peptide alignment can be typed in text box or uploaded from the file and can not contains fully gaped columns. ELM database can be searched to obtain the alignment of ELM motif as input. See details below.

Upon submitting the alignment, the default PSSM for input peptides will be derived and list of options will be displayed. On this page, the user can change the scoring method (see full list here), manually modify PSSM and set the search options.

Peptides

Set of aligned peptides in fasta or text format derived by user. Can be entered in text box or loaded from file.

Format Example
Text AVEQTPRK
SVEQTPRK
SVEQTPKK
Fasta >ELMI001940
AVEQTPRK
>ELMI001939
SVEQTPRK
>ELMI001938
SVEQTPKK

ELM motifs

Aligned ELM instances of ELM motif class can be retrived from ELM database by using search box on input page. Start typing the ELM class name and choose the motif from dropdown list.

Options

Option Default Description
species Homo sapiens Species proteome to search for PSSM matches.
motif computed Motif consensus used in conservation scores calculation and taxonomic range analysis. Motif can be manually edited, see details here.
flank length 5 The length of surrounding residues at both sides of motif. Range: 0-20.
disorder cut-off 0.4 Mean IUPred scores of motif residues used to filter structured regions. Range: 0-1.
p-value cut-off 0.001 Used as cut-off for significance of PSSM matches to filter irrelevant matches. Calculated as probability of achieving as good or better score than background model. Range: 0-1.
proteome order reverse Order of proteome scanning to obtain background distribution of scores used to compute PSSM p-value. One of: reverse, shuffle or forward.
mask cut-off computed Mask residues in motif sequences below defined cut-off to highlight relevant amino acids in motif. All residues in sequence with score < cut-off are replaced with ".". Default computed as the lowest score for specific-position residue from the input alignment.
taxonomic range motif Method to define whether peptide from the alignment is conserved. One of: motif, PSSM, both (PSSM + motif). Description of methods is provided here.
conservation p-value cut-off 0.001 Cutoff used in decision whether peptide from the alignment is conserved. Works if taxonomic range is computed based on PSSM method.
shared annotations empty Set of proteins used to obtain significant shared ontology with peptide instances obtained from scanning. The same set of proteins is used to determine whether interaction between obtained results and set of provided proteins exist.
shared annotations p-value cut-off empty Used as cut-off for significance of shared ontology. Calculated as probability of sharing a given term by any two proteins in proteome by chance used to filter common shared annotations. Range: 0-1.

Motif

PSSM is derived with computed motif based on statistical significance and rules described in supplementary material in paper. The motif is represented as regular expression and can be edited by user. The characters allowed to build the regular expression are listed below:

Character Name Meaning
D, E, K, R, H, S, T, C, M, N, Q, F, Y, W, G, A, V, L, I, P residue One amino acid
. or X dot Any amino acid allowed
[...] character class Amino acids listed are allowed
[^...] negated character class Amino acids listed are not allowed
{ min, max } specified range Matches min to max repetitions of the previous amino acid. Min required, max allowed
^ caret Matches the amino terminal
$ dollar Matches the carboxy terminal
| pipe Denotes alternation. For example (KL)|(LK), will match either KL or LK.
() brackets Group items into a single logical item. The bracket indicates the start and end of the group.
Examples
Name Motif
KEN box motif KEN
Cyclin-binding RxL motif [KR].L.{0,1}[LF]
C-terminal KDEL Golgi-to-ER retrieving signal [KRHQSAP][DENQT]EL$
N-terminal myristoylation site ^M{0,1}G[^EDRKHPFYW]..[STAGCN][^P]

Modification of the PSSM

The PSSM can be modify by changing the scoring method (default: PSI-BLAST IC) and/or by manual interaction with PSSM represented as heatmap on the input page. See details below.

Scoring methods

PSSM can be computed using different scoring methods. Available scoring schemas with short description are listed below. Full description with equations are provided in Supplementary material of the article.

Scoring method Description Reference
PSI-BLAST Modified PSI-BLAST algorithm to motif searches. 9254694 19088134 11452024 16218944
PSI-BLAST IC Modified PSI-BLAST algorithm and adjusted with information content. 9254694 19088134 11452024 16218944
MOTIPS Adopted MOTIPS method to derived a PSSM and scoring peptides. 20459839
Log odds Logarithm base 10 of binomial statistics of enriched versus depleted residues at specific positions. 24097270
Log Relative Binomial Logarithm base 10 of probability of over or under-representation of residues at specific positions. -
Ratio Amino acids frequencies normalized by background model at specific positions. -

In addition to these score, we added "frequency" and "counts" for a visualisation purpose only.

Background distribution

For each species the amino acid composition of the proteome has been computed using different disorder thresholds. It's possible to choose the frequencies used as background distribution by selecting the species and the disorder cut-off. Disorder cut-off means that amino acid frequencies were computed from the proteome residues with IUPred score greater than selected cut-off. By default, "Homo sapiens" and a disorder cut-off of 0.5 are selected.

Additionally, for the PSI-BLAST/PSI-BLAST IC methods, two parameters (i.e. lambda and max independent observation) were precomputed based on background frequencies.

Manual modification of the PSSM by clicking on the heatmap

modification PSSM
The APC/C D box degrons motif was modified as follow:
  1. the two positions at the extremities were zeroed by clicking on their position number (1, 2, 22, 23)
  2. the arginine at the position 9 was marked as "required" (all other amino acids at this position are marked as "prohibited" and receive a very negative score) by choosing the "require" action and clicking on the tile at the position 9xR.
  3. The score of the Leucine and Phenylalanine at the position 12 were grouped by choosing the action "group (max)" and by clicking on the tiles at the positions 12xL and 12xF

The PSSM visualised as a heatmap is interactive. Hovering with the mouse cursor will display more information, clicking on a tile will modify it. This can be use to further define the motif. 4 actions are possible, listed below, a dropdown menu allows the user to change the action before clicking on a tile. Clicking on the position number, at the top of the heatmap, will nullify (put zeros) for every amino acid at the position.

Multiple modifications can be applied at one position, but only one per amino acid per position. Modifications are displayed on the heatmap itself and the sequence logo above it is updated. Modifications can be reverted by clicking again on a tile or by clicking on the reset button.

Option Description
require Requiring a amino acid will fix its score and prohibit the others. Multiple amino acids can be "required" at one position, the relative importance of each of them will be conserved.
prohibit A "prohibited" amino acid will take a very low and negative value at this position (equal to -1000).
group Grouped amino acids at one position will take the same scored value. 2 ways of grouping are implemented: sum of all the grouped residues scores at the position and the maximum scores of these amino acid at this position.
zero The scores are replaced by zeros.

Output

After a job is finished the main result table will be displayed. The PSSM matches with statistical significance metrics, overlapping feature and motif attribute annotations will be presented in the table on Instances page. Next, the obtained results can be filtered by discriminatory attributes and/or used to run evolutionary and functional enrichment analysis.

The evolutionary analysis allows looks in depth for instances conservation across different species and conservation of motif sequence context (Conservation page).

Functional analysis performs enrichment analysis of functional annotations to indicate possible motif function, localisation or binding partner (Function page).

Filtering can be performed based on different information such as: accessibility, taxonomic range, interacting partners, subcellular localisation and functional annotations (Filters page), or shared annotations with a hub protein (Hub page).

Instances

Instance page displays the results obtained from a scanning the proteome with generated PSSM on the input page. The best matches (below PSSM p-value cut-off, maximum 10000) are annotated with peptide, motif attributes and feature information. Depending on the input options and/or applied filters the shared annotations and functional annotations are listed in the result table. Furthermore, the instances are flagged with warnings if occur in the inaccessible regions. Short explanation of each column is presented in table below.

Additionally, each motif instance is linked to ProViz - a visualisation of the motif sequences with protein annotations and alignment tool.

instances page
Instances page.
  1. Consensus used in conservation analysis.
  2. Shared annotations with a hub protein - shown if protein was defined.
  3. PSSM statistics, PSSM p-value used as cut-off for returned hits.
  4. Motif attributes: conservation (calculated based on consensus (1)) and accesibility.
  5. Feature annotations.
  6. Quick filtering based on warnings and shared annotations.

Table

Category Column Description Link
Peptide Virus Virus species. The column is showed only if search was against Viruses proteomes. -
Protein Name Protein and gene name. Information about overlapping instances and warnings. UniProt
Peptide A motif sequence with the flanks. Flanks are displayed as lowercase residues. Masked sequence appears when hover over peptide.
means that the peptide is an exact match of one of peptides used to build a PSSM.
Peptide length is always equal to PSSM length, and in special cases (motif found in N-, C- termini proteins) can be represented as "XX--", where X denotes amino acid and "-" gap character for PSSM length equal 4.
ProViz
Start Start position of the motif in protein. -
End Stop position of the motif in protein. -
Motif attributes PSSM P-value Statistical significance of peptide according to the background model. Lower score better. PSSM score and rank are displayed when hover over the p-value.
Bolded, green values indicate that peptide obtained better score than the best score from background model.
-
Disorder score Mean IUPred score. High scoring peptides are less likely to be in a globular region. -
Conservation Conservation score. Lower scores indicate more conserved peptides across the alignment. ProViz
Features Domain Overlapping regions with domains. Pfam and UniProt
Structure Overlapping regions that have structure solved by NMR or X-ray crystallography. PDB
Secondary Structure Overlapping regions that have been shown to form secondary structure. UniProt
Motif Overlapping regions with experimentally validated short linear motifs. ELM and UniProt
Region Overlapping regions with experimental evidence for function. UniProt
Switch Overlapping curated experimentally validated motif-based molecular switches. UniProt
Modification Overlapping regions with sites of post-translational modifications. PhosphoSite, phospho.ELM and UniProt
Topology Overlapping region topology information. UniProt
Isoform Overlapping splice variants. UniProt
Mutagenesis Overlapping mutated residues which alter function. UniProt
SNP Overlapping single nucleotide polymorphism with disease association and genotype information. dbSNP, 1000genomes and UniProt
Other Overlapping other features of interest. UniProt
Functional annotations GO terms Gene ontology terms for protein containing peptide. Gene Ontology
Keywords UniProt keywords for protein containing peptide. UniProt Keywords
Interactors: Proteins Proteins experimentally shown to interact with the protein containing peptide. UniProt
Interactors: Families Protein families interacting with the protein containing peptide. UniProt
Interactors: Domains Domains found in proteins which interact with the protein containing peptide. Pfam
Shared annotations Interaction Indicate if protein-protein interaction exists between instance and user-defined set of proteins. -
Shared ontology Shared GO terms with user-defined set of proteins. Displayed in three categories: localisation (L), molecular function (F) and biological process (P). Hover to see the least likelihood shared GO term or click to see other shared GO terms. -

Instance annotations

The instances are provided with several annotations such as motif attributes, feature, hub and function annotations.

Motif attributes

Motif attributes annotations include computed scores based on peptide conservation, accessibility and similarity to PSSM. The most important attributes are showed in the result table. Attributes not listed in table can be found in downloaded files. The descriptions of these calculation are listed in the table below.

Motif attribute Description Range
PSSM P-value Calculated as a probability that observed value can achieve the same or better score than the background model. Background model is obtained as distribution of scores from scanning the target proteome in reverse, shuffle or forward order. Lower score indicates that the peptide is more similar to the peptides used in creation of PSSM. 0-1
Disorder score IUPred score computed as mean of IUPred scores across residues of motif consensus. Lower score, more globular region. 0-1
Conservation score Relative conservation score computed across the defined residues of motif consensus as described for SLiMPrints tool. Lower score, more conserved region. 0-1
Surface accessibility score Proportion of the peptide that is accessible to water molecules in a solved structure of the region. 0-1
Anchor score Anchor score computed as mean of Anchor scores across residues of motif consensus. Lower score, higher propensity to fold upon binding. 0-1
Feature annotations

Overlapping feature annotations with peptide are grouped into 12 different types. A number in a feature column indicate how many features were found. To see more details, expand feature column by clicking on above column name. To hide these information, click again on the button.

All feature columns can be expanded/collapsed at once by clicking expand/collapse button above feature column names.

Hover over the feature to see start and stop position and more information of each feature. Additionally, each feature is provided with distance information. For example, distance -2 means that annotated feature stops 2 residues before motif start position in the flanking region. No information about distance indicates that annotated feature directly overlaps motif consensus. To see more details about each feature, click on feature of interest and you will be redirected to the source website.

Shared annotations (hub)

Information about shared annotations is shown in table only if set of proteins was provided on input page in shared annotations section.

Shared annotations are grouped into interaction and ontology group and indicate if interaction exist between the instance and set of proteins and if they share any significant GO term. The shared ontology is provided with a p-value which indicate the significance of sharing this GO term by any two protein in the proteome by chance. The least likely shared GO term appears when hovered over the one of icon: localisation (L), biological process (P) or molecular function (F) and full list of significant shared annotations between instance and defined proteins will display when icon is clicked.

Full list of significant shared annotations for all instances can be seen in hub tab and specific annotations can be used in filtering.

Functional annotations

Information about functional annotations is shown in table only if instances were filtered based on these annotations (see Filters section). Annotations are grouped into ontology and interaction annotations (see details). The functional data are obtained from Gene Ontology, UniProt, IntAct and HIPPIE databases.

Warnings

The instances are flagged to warn user if a given peptide is inaccessible to intracellular proteins. Instances with warnings are shown with yellow background colour in the result table and icon next to protein name. Hover over the icon to get more information about warning details.

Warnings are grouped into two types based on background colour in the result table: domains and other.

Domain warnings means that peptide overlaps region with domain(s) and other warnings are listed in table below.

Warning Description
Disorder Instances with disorder score ≥ 0.4.
Surface accessibility Instances with surface accessibility percent score < 50% i.e. less than 50% of the peptide is accessible to water molecules in a solved structure of the region.
Localisation Instances with Gene Ontology terms which indicate extracellular localisation.
Topology Instances overlapping topology features which exclude intracellular regions.
instances page - warnings
Instances page - warnings.

Filtering

The instances can be quick filtered based on warnings and hub annotations. To filter results click on above the table in the right corner and switch on/off the slider next to warning/hub type.

instances page - filtering
Instances page - filtering. Switched off warnings exclude instances with warnings. Switched on shared annotations include instances which share min. 1 annotations with a hub protein.

The advanced filters options are available on Filter and Hub page.

Download

The results can be saved as tab separated (tdt) or JSON format by clicking on the button in the top left corner of table. Information about ontologies and interactions are not provided in tdt format and hub annotations are limited only to the best terms to reduce the size of file and be easier to read. All information can be easily find in JSON format.

Tab separated format

Columns with description are shown in the table below. If a score could not be calculated for motif attribute, then -1 score occur in the file. For feature annotations, each feature in column is separated by ";".

Column Description
InstanceId Unique instance identifier.
ProteinAcc UniProt protein accession.
ProteinName Protein name.
GeneName Protein gene name.
Hit Motif sequence with flanking regions. Flanks are represented as lowercase residues.
SeqStart Motif start position in protein.
SeqStop Motif stop position in protein.
IUPred Disorder score.
Anchor Anchor score.
SA Surface accessibility score.
Conservation <alignment> (score) Conservation score across <alignment>.
Conservation <alignment> (var) Conservation variance across <alignment>.
Domain Format: <name>|<id>|<start>|<stop>|<distance>
Motif Format: <name>|<id>|<start>|<stop>|<distance>
Modification Format: <name>|<enzymes>|<pmids>|<description>|<id>|<start>|<stop>|<distance>
Structure Format: <name>|<resolution>|<method>|<chain>|<start>|<stop>|<distance>
SNP Format: <name>|<variant>|<id>|<start>|<stop>|<distance>
Mutagenesis Format: <name>|<mutation>|<id>|<start>|<stop>|<distance>
Region Format: <name>|<start>|<stop>|<distance>
Topology Format: <name>|<start>|<stop>|<distance>
Secondary Structure Format: <name>|<start>|<stop>|<distance>
Isoform Format: <name>|<variant>|<start>|<stop>|<distance>
Switch Format: <type>|<subtype>|<mechanism>|<id>|<start>|<stop>|<distance>
Other Format: <name>|<start>|<stop>|<distance>
Warnings Format: <Warning_type>:<warning details>
Shared_interaction Format: <protein_name (protein_acc)>
Shared_function_terms Format: <GO term name (id)> shared_with:<protein_name (protein_acc)>
Shared_function_sig Probability score
Shared_function_terms Format: <GO term name (id)> shared_with:<protein_name (protein_acc)>
Shared_function_sig Probability score
Shared_process_terms Format: <GO term name (id)> shared_with:<protein_name (protein_acc)>
Shared_process_sig Probability score
Shared_localisation_terms Format: <GO term name (id)> shared_with:<protein_name (protein_acc)>
Shared_localisation_sig Probability score
JSON

Full list of fields for each instance is in the table below. If motif attribute score could not be computed, then -1 score is provided. The feature field(s) are present in results only if there is a one or more feature(s) overlapping motif consensus.

Field Type Description
instanceId Integer Unique instance identifier.
ProteinAcc String UniProt protein accession.
ProteinName String Protein name.
GeneName String Protein gene name.
Hit String Motif sequence with flanking regions. Flanks are represented as lowercase residues.
SeqStart Integer Motif start position in protein.
SeqStop Integer Motif stop position in protein.
IUPred Float Disorder score.
Anchor Float Anchor score.
SA Float Surface accessibility score.
Conservation <alignment> Object Conservation score and variance across <alignment>. Format: {"score": <float>, "var": <float>}
GOterms List of objects List of GO terms. Format: [{"id": <GOterm id>, "name": <GOterm name>}
Keywords List of objects List of UniProt keywords. Format: [{"id": <keyword id>, "name": <keyword name>}
Interactors List of objects List of interacting proteins with protein containing motif. Format: [{"id": <UniProt protein accession>, "name": <UniProt protein name (gene name)>}
Domain List of objects Format: see features
Motif List of objects Format: see features
Modification List of objects Format: feature format, see below..
Structure List of objects Format: see features
SNP List of objects Format: see features
Mutagenesis List of objects Format: see features
Region List of objects Format: see features
Topology List of objects Format: see features
SecondaryStructure List of objects Format: see features
Isoform List of objects Format: see features
Switch List of objects Format: see features
Other List of objects Format: see features
Warnings List of objects List of warnings. Format: [{"name": <warning category>, "reason": <warning reason>}]
shared_ontology Dictionary
Features
Field Type Description
name String Feature name.
url String Link to source data.
description Object Format: {"start": <feature start position>, "stop": <feature stop position>, "distance": <distance to motif consensus>, "description": <other specific information in JSON format>}

Conservation

There are two main evolutionary sections: flank conservation and taxonomic range for each available clad. Clads depend on the query species and include: QFO (Quest for Orthologs), Arthropoda, Viridiplantae, Amoebozoa, Fungi, Nematoda, Metazoa, Saccharomycetales and Viruses. Each conservation section is provided with general peptide and specific conservation data. Short description of each column is listed in the table below.

To change evolutionary section or clad select one from navigation menu above the table or in sidebar. The custom view of table columns can be set in sidebar. Notice that not all available columns are shown in table by default.

Flank conservation

Instances are annotated with the relative conservation scores for each residue in PSSM match and flanking regions (always from -10 to +10 residues). The conservation of each residue is represented with colour intensity i.e. more intense red colour means more conserved residue. Several scores are computed to compare conservation of motif sequence to flanking regions which are listed in the table below.

conservation page - flanks
Conservation page - flank conservation view. Residues of PSSM match with flanking regions on both side (-10/+10). More red, more conserved residue.

Taxonomic range

Instances are annotated with the information about the motif conservation across a species from the alignment. Peptide conservation is estimated based on: motif, PSSM statistics or combined method, which is defined on input page by user (default: motif). Each peptide from the clad alignment is marked as conserved (C), non-conserved (N) or missing in the alignment (X).

Motif method: conservation is defined with use of motif consensus represented as regular expression defined on input page. The peptide from the alignment is marked as conserved if match the motif consensus at the same position as query species motif.

PSSM method: conservation is calculated with use of PSSM scoring method. The peptide at the same position as query species motif from the alignment is scored with the same PSSM as used in search and assigned with PSSM p-value. If the p-value of peptide is less than user-defined cut-off (conservation PSSM p-value cut-off) then the peptide is marked as conserved.

Combined method: the instance is conserved if meet both criteria: consensus match and conservation p-value cut-off.

Usually only the subset of species is default shown in the result table. To see full list of species or customize table columns, use sidebar.

conservation page - taxonomic range
Conservation page - taxonomic range view. Conservation across set of species from an orthologue alignment. Instances can be: conserved (C), non-conserved (N) or missing in the alignment (X).

Table

View Column Description Shown by default
Both Protein Name Protein name and gene name. +
Peptide Peptide sequence with flanks. +
Start Peptide start position in protein. +
Stop Peptide stop position in protein. +
Disorder score Motif attribute calculated as mean IUPred score across peptide. +
Domain Overlapping regions with domains. +
Motif Overlapping regions with curated short liner motifs. +
Con Score Combined Conservation score combined. It is sum of conservation score and conservation variation. +
Flank conservation Sig conserved residues defined positions Proportion of residues in the defined positions of a motif that are significantly conserved (p > 0.05). -
Sig conserved residues Flanks Proportion of residues in the flanking positions of a motif that are significantly conserved (p > 0.05). -
Sig conserved residues Ratio The ratio of Sig conserved residues defined positions to Sig conserved residues Flanks. +
L-10:L-1 Conservation scores and residues for N-terminal flank. +
P<motif position> Conservation scores and residues for motif consensus. +
R1:R10 Conservation scores and residues for C-terminal flank. +
Taxonomic range Conserved Counter Number of species in which the motif consensus is conserved at the same position as the query species motif. +
Species columns Shows if the peptide from the alignment is conserved (C) or not (N) at the same position as the query species motif in each species of the select clade. If no data is available (i.e. there is no protein in the alignment for the species) an "X" is supplied. +

Sidebar

The Options panel is located on the left and there are three sections: Views, Columns and Save.

Views

In Views section a view can be changed. Switch from current view to Taxonomic range or Flank conservation section and specify the alignment. You can do the same from navigation menu above the result table.

Columns

In Columns section the columns can be switched on/off to hide/show them in the result table. Here, you can see full list of species available in selected alignment. To add column in the result table, just tick the checkbox . The table will be updated automatically.

Save

In Save section the results can be downloaded as tab separated (tdt) or JSON format. See Download for more details.

sidebar
Sidebar. There are three sections: Views, Columns and Save to change view or download results.

Download

The results can be saved as tab separated (tdt) or JSON format. To download results, use sidebar (Save section).

Tab separated format

Columns with description are shown in the table below. If a score could not be calculated for motif attribute, then -1 score occur in file.

Column Description
InstanceId Unique instance identifier.
ProteinAcc UniProt protein accession.
ProteinName Protein name with gene name.
Hit Motif sequence with flanking regions. Flanks are represented as lowercase residues.
SeqStart Motif start position in protein.
SeqStop Motif stop position in protein.
IUPred Disorder score
Domain Domain names separated by ";".
Motif Motif classes separated by ";".
<alignment> conservation score Conservation score across <alignment>.
<alignment> conservation var Conservation variance across <alignment>.
<alignment> conservation combined Conservation score combined. Sum of conservation score and variance across <alignment>.
conserved_counter Number of conserved species across <alignment>.
<species> C, N or X. C - the motif consensus is present at the same position as query species (conserved). N - the motif consensus is missing at the same position as query species (non-conserved). X - species is not present at the alignment (missing).
mean_flanks Mean of relative conservation scores across residues of flank regions.
var_flanks Variance of relative conservation scores across residues of flank regions.
Sig conserved residues defined positions Proportion of residues in the defined positions of a motif that are significantly conserved (p > 0.05).
Sig conserved residues Flanks Proportion of residues in the flanking positions of a motif that are significantly conserved (p > 0.05).
Sig conserved residues Ratio The ratio of Sig conserved residues defined positions to Sig conserved residues Flanks.
L-10:L1 The relative conservation scores for residues in N-termini flank.
L<position> The relative conservation scores for residues in motif consensus.
R1:R10 The relative conservation scores for residues in C-termini flank.
Alignment Hyperlink to ProViz visualisation tool.
JSON

Full list of fields for each instance is in the table below. If motif attribute score could not be computed, then -1 score is provided.

Field Type Description
instanceId Integer Unique instance identifier.
ProteinAcc String UniProt protein accession.
ProteinName String Protein name.
GeneName String Protein gene name.
Hit String Motif sequence with flanking regions. Flanks are represented as lowercase residues.
SeqStart Integer Motif start position in protein.
SeqStop Integer Motif stop position in protein.
IUPred Float Disorder score.
ConservationScore Float Conservation score.
ConservationVar Float Conservation variance.
ConservationScoreCombined Float Conservation score combined. Sum of conservation score and conservation variance.
Conservation_Scores List of objects Conservation score and variance across <alignment>. Format: [{"<searchdb>": {"score": <float>, "var": <float>}}].
Domain List of objects Format: feature format, see features.
Motif List of objects Format: feature format, see features.
mean_flanks Float Mean of relative conservation scores across residues of flank regions.
var_flanks Float Variance of relative conservation scores across residues of flank regions.
flank_sig Float Proportion of residues in the flanking positions of a motif that are significantly conserved (p > 0.05).
motif_sig Float Proportion of residues in the defined positions of a motif that are significantly conserved (p > 0.05).
ratio_sig Float The ratio of Sig conserved residues defined positions to Sig conserved residues Flanks.
motif_sig_pos List of Integer The defined positions of a motif consensus.
conserved_counter Integer Number of conserved species i.e. motif consensus is at the same position as query species.
Conservation List of objects Species conservation. Format: [{"species_code": Boolean}]. True - motif consensus is present at the same position, False - motif consensus is missing at the same position.
flank_residues List of objects Conservation for each residue in flanking regions. Format: [{"<flank position>": {"aa": <residue>, "score": <relative conservation score>}}].
peptide_residues List of objects Conservation for each residue in motif consensus. Format: [{"<motif position>": {"aa": <residue>, "score": <relative conservation score>}}].
proviz_link String Link to ProViz visualisation tool.

Function

The table contains the results of enrichment analysis of Gene Ontology terms, UniProt keywords and interaction data. Three following approaches are available to performed enrichment analysis: enrichment analysis with motif search space correction where search space is limited to disordered regions of proteome, enrichment analysis based on conservation where conservation scores are used as the ranking criteria and classical enrichment analysis. All approaches accounts for evolutionary relationship of proteins by grouping similar proteins based on sequence and function similarity.

function page
Function page.
  1. Sidebar.
  2. Cut-offs to limit returned hits. Cut-off is based on adjusted p-value (motif search space method), and conservation cut-off means minimum one p-value from conservation clad meet the cut-off criteria.
  3. Box for searching terms of interest and filtering panel to limit motif instances mapped to selected terms from table.
  4. Filters results in the table based on terms enrichment.
  5. Statistics results from motif search space correction method.
  6. Statistics results from conservation method. (if conservation method is turned on)

Approaches

Enrichment analysis with motif search space correction

Enrichment analysis with motif search space correction is improvement of classical approach. It accounts for search space, i.e. the analysis is limited to disorder regions of proteome, in the same way like search space for motif searches (disorder cut-off). The enrichment calculations try to answer the question: what is a probability that more than m instances of all motif instances in the dataset (M) belong to a given functional term shared by n of N disordered residues in the entire proteome? Disordered residues are residues with score ≥ than disorder cut-off.

The enrichment analysis uses Hypergeometric test with Benjamini-Hochberg correction to define significance. Details of calculation can be found in SLiMSearch Supplementary Material or on the SLiMSearch help page.

Enrichment analysis based on conservation

Enrichment analysis based on conservation uses relative conservation scores as ranking criteria. The conservation scores of motif instances are assigned to functional annotations. For each term, the conservation scores assigned to a given term are compared to remaining conservation scores i.e. which are present in results, but not assigned to that term, using the Mann Whitney U test. The functional annotations assigned to more conserved instances will be more related to biological function of motif compared to these functional annotations which are assigned to instances with randomly distributed conservation scores. The enrichment analysis is performed on all available alignments for conservation data. By default, this analysis is not performed. To run them, set Conservation to True in Options section in sidebar and click Search button.

Enrichment analysis based on classical approach

Enrichment analysis based on classical approach use hypergeometric distribution to identify enriched functional annotations and try to answer the question: what is a probability that more than m instances of all instances in the dataset (M) belong to a given functional term compared to a background distribution, where the background distribution is proportion of proteins with a given term to all proteins in the entire proteome.

The enrichment analysis uses Hypergeometric test with Benjamini-Hochberg correction to define significance. Details of calculation can be found in SLiMSearch Supplementary Material or on the SLiMSearch help page.

Benjamini-Hochberg correction for multiple hypothesis testing

The correction is applied in each category (i.e. Biological process, Molecular function, Localisation etc.) and it is calculated as: q=(p*i)/n, where p is p-value, n is the number of terms in category and ith term ranked according to the p-value in category.

Clustering based on evolutionary relationship

The enrichment analysis are corrected for evolutionary relationship based on sequence and function similarity. Proteins containing consensus matches can be grouped together based on different UniProt clusters (UniRef50, UniRef90, UniRef100), UniProt protein families or corrected cluster. Corrected cluster combines UniRef50 and UniProt protein families' clusters. There is also options not to cluster the data. The default cluster option is set to UniRef50. These can be change in sidebar in Options section.

Details about calculation with cluster options are described in SLiMSearch Supplementary Material.

Results

Results of enrichment analysis are grouped in two sections: ontology and interaction.

Ontology section is classified into 5 categories: TOP (the most significant 20 terms), biological process, molecular function, localisation and disease.

Interaction section is divided into 3 groups: Domain - domains found in interacting proteins, Family - interacting proteins grouped into protein families, and Protein - interacting proteins.

The terms are highlighted with different colours to make results more readable. The meaning of each colour is listed in table below. Furthermore, results are marked with warnings whether it is possible that a given term is overestimated. The result table can be searched by term name and filtered by enriched, depleted or flagged with warnings terms ( right corner above the result table). The results can be downloaded as tab separated (.tdt) of JSON (.json) file. Short description of each column in result table can be found here.

Colour Meaning
Green Significant terms with adjusted p-values < 1e-4.
Grey Enriched terms i.e. with enrichment score (E) > 1.
Blue Depleted terms i.e. with enrichment score (E) < 1.
Light yellow Term is flagged with repeat OR cluster flag.
Dark yellow Term is flagged with repeat AND cluster flag.
Result table
Column Description Shown by default
Category Term category. -
ID Unique term identifier. +
Name Functional annotation name. +
# Number of motif instances that map to this term. +
# motifs Number of motif instances in dataset. -
# residues Number of disordered residues* that map to this term. -
# residues proteome Number of disordered residues* in whole proteome. -
# Proteome Number of proteins in proteome that map to this term. +
Enrichment Enrichment (E). If (E) > 1 then term is enriched, otherwise is depleted. +
P-value Enrichment significance calculated using Hypergeometric test. Lower scores, more enriched/depleted term. +
Adj pval Adjusted p-values. P-values after BH correction. +
<alignment> P-value Enrichment significance calculated based on conservation. +
Warnings

The functional annotations are flagged to warn user if a given term can be overestimated. The terms with warnings are shown with yellow background in the result table and icon next to adjusted p-value value. To see details about warning, hover over the icon. There are two types of warnings: repeat and cluster flag.

Flag Name Description
repeat flag The term can be overestimated when motif instances occur multiple times in the same protein due to repeated regions in that protein. The term is flagged if the number of repeated instances is significantly greater than expected (i.e. p < 0.001).
cluster flag The term can be overestimated when motif instances occur in related proteins, but were not clustered based on evolutionary relationship. This flag is only calculated when enrichment analysis is performed on UniRef50 clusters. The term is flagged if the ratio of number of corrected clusters assigned to a term to UniRef50 clusters assigned to this term is ≤ 0.5.
Filtering

See Filters.

Sidebar

The Options panel is located on the left.

Section Description
Views A view can be changed to see enriched terms from selected category.
Options Cluster UniProt Reference Cluster (UniRef) utilised for the analysis. Default: UniProt50
Conservation Compute enrichment significance based on conservation scores. Default: false
P-value P-value cut-off limits number of returned hits. Default: 0.01
Columns The columns can be switched on/off by ticking the checkbox next to column name. The table will be updated automatically.
Save The results can be downloaded as tab separated format (tdt) or JSON format
function page - sidebar
Function page - sidebar. There are four sections to change current view, rerun job with different options or download results:
  1. View
  2. Options
  3. Columns
  4. Save

Download

Tab separated format
Column Description Approach
Category Term category. all
ID Unique term identifier. all
Name Functional annotation name. all
No. of motif instances mapped to term in dataset (m) Number of motif instances mapped to a given term in dataset (m). search space correction
No. of motif instances in dataset (M) Number of motif instances in dataset (M). search space correction
No. of disordered residues mapped to term (n) Number of disordered residues mapped to a given term in proteome (n). search space correction
No. of disordered residues in proteome (N) Number of disordered residues in proteome (N). search space correction
Enrichment Enrichment score (E). search space correction
Pvalue Enrichment significance. search space correction
Adj pvalue Corrected p-value for multiple hypothesis testing. search space correction
No. of proteins mapped to term in dataset Number of proteins mapped to a given term in dataset. classical
No. of proteins mapped to term in proteome Number of proteins mapped to a given term in proteome. classical
No. of proteins in dataset Number of proteins in the dataset. classical
No. of proteins in proteome Number of proteins in the entire proteome. classical
Enrichment (Proteins) Enrichment score (E). classical
Pvalue (Proteins) Enrichment significance. classical
Adj pvalue (Proteins) Corrected p-value for multiple hypothesis testing. classical
Repeat flag Warning. Overestimation of term (True/False). all
Cluster flag Warning. Overestimation of term (True/False). all
Repeat flag (expected) Expected number of instances to be seen by chance mapped to a given a term. all
Repeat flag (expected p-value) Significance of repeat flag. all
Cluster flag (ratio) Significance of cluster flag. all
<alignment> Enrichment significance. conservation
JSON
Field Type Description
category String Term category.
id String Unique term identifier.
name String Functional annotation name.
count Float Number of motif instances mapped to a given term in dataset.
M Float Number of motif instances in dataset.
n Float Number of disordered residues mapped to a given term in proteome.
N Float Number of disordered residues in proteome.
enrichment Float Enrichment score (E) for motif search space correction approach.
pval String Enrichment significance for motif search space correction.
pvalBH String Adjusted p-value for multiple hypothesis testing for motif search space correction.
proteinTerm Float Number of proteins mapped to a given term in dataset.
occurrence Float Number of proteins mapped to a given term in proteome.
proteinCount Float Number of proteins in the dataset.
proteinBackgroundCount Float Number of proteins in the proteome.
flag Boolean Repeat flag.
expected Float Expected number of instances to be seen by chance mapped to a given a term.
exp_pval Float Significance of repeat flag.
flag2 Boolean Cluster flag.
countUniMix Float Significance of cluster flag.
url String Link to source data.

Hub

This functionality is optional and is available when the hub protein was specified on input page - shared annotations in advanced options section.

Shared annotations with a hub protein are grouped into two sections: Ontology and Interaction.

Ontology

Shared functional annotations with motif partner(s) provided on the input page are displayed in the table.

GO terms with p-value equal or below user-defined cut-off are annotated with significance metrics and interacting proteins/instances. These GO terms can be used to filter motif instances.

By default, number of interactors, proteins containing motif and motif instances are listed in the table, and details i.e. protein names can be seen by clicking on expand button above column name.

The GO terms can be filtered based on categories by clicking on icon above the right table corner. Just switch on/off the slider next to the category of interest and the table will be updated automatically.

Specific GO terms can be searched in the table by using search box above the table. To search a term, start typing the name in the provided box and the table will be updated automatically.

Short descriptions of table columns are listed below.

Filtering

To filter motif instances based on shared functional annotations, tick the checkbox next to terms () and click Filter button to filter instances and be redirected to Instance page, or click Add button to save the filter.

hub page - ontology
Hub page - ontology view.
  1. Search for a specific term(s) by typing in the provided box.
  2. Select the terms of interest using provided checkbox next to term name and click on Filter or Add button to limit motif instances to these mapped to the selected terms.
  3. Filter the table based on GO term category.
Table
Name Description
Category GO term category.
Name Name of GO term with link to a source.
Prob (proteins) Probability of sharing a term by any two proteins in the proteome by chance. Used as significance cut-off.
Prob (UniRef50) Probability of sharing a term by any two proteins clustered based on UniRef50 clusters in the proteome by chance.
Interactors Interacting proteins (defined by user on the input page) that shared a specific term.
Proteins Protein containing motifs that shared a specific term.
Instances Motif instances that shared a specific term.

Interaction

Displays the list of proteins containing motif which are known interactors of motif partner(s) defined by user on the input page.

Short descriptions of table columns are listed below.

hub page - interaction
Hub page - interaction view.
  1. Select the proteins of interest using provided checkbox next to protein name.
  2. Click on Filter or Add button to limit motif instances to these occuring in the selected proteins.
Table
Name Description
Name Protein containing motif(s) which interact with set of provided proteins on the input page.
Interactors Interacting proteins (i.e. defined by user on input page) with protein containing motif.
Instances Motif instances which interact with set of provided proteins on the input page.

Filters

Overview

Motif instances can be filtered based on motif attributes, protein-containing, ontology or hub annotations. The filters are grouped into following categories:

Filter Description
Hub protein Shared functional annotations and interactors of motif binding-partner.
Hub domain Interacting domains.
Annotation Subcellular localisation and enriched functional annotations in the dataset.
Evolution Taxonomic range. Conservation across different clads/species.
Accessions Containing protein and ontology or interacting annotations.
Accessibility Accessibility to intracellular proteins.
Shared annotations Shared ontology and interaction with set of proteins predefined by user.

Important! After filtering, the results on Instance, Conservation and Function page will be shown only for instances that meet that criteria. For example, functional enrichment analysis will be recalculated for new motif dataset and conservation information will be limited to instances after filtering.

Adding a filter

To filter instances, choose one of filtering options from navigation menu and follow the instruction provided on page. All filtering sections have Description header with [-] or [+] sign. The short description of filtering can be expanded or collapsed by clicking on these signs. After specifying your filters click Filter button and you will be redirected to Instances page to view filtered instances. You can save your filter by clicking on Add button. The filter will be added to all filters and you can specify another filtering options.

Using multiple filters

The instances can be filtered by multiple filters. To specify your filters, use Add button or filter instances with Filter button and come back to another filter and click again Filter button. The next filter will be added and two filters will be used.

To display details about each filter, click on the "details" button next to the filter name. Each filter can be removed by clicking on the icon next to filter name. After removing filters, click on the "UPDATE" button and the motif instances will be filtered with updated filters. If you remove all filters, the results will be updated automatically. If you do not want to make any changes in filters, click on "Instances" tab from navigation to see instances that meet multiple criteria.

Filtering
Applying multiple filters.
  1. Filters header - expanded.
  2. Details about filter (to see, click on details button).
  3. Remove filter (click on icon).
  4. Update results with new filtering options (click UPDATE button - only after removing filter(s)).
  5. iew consensus matches that meet specified criteria.

Hub protein

There are two options to filter instances based on annotations of known motif binding partner. The instances can be filtered based on shared functional annotations or presence as interactors for binding partner.

Shared functional annotations

The functional annotations of binding partner are provided with information how likely a given term is shared by any two proteins in the proteome. The probabilities are computed based on UniRef50 clusters (Sig (UniRef50) column) and without any clustering (Sig (NoClustering) column). The user can limit the number of returned functional annotations to these more specific by setting cut-off to lower score. The lower cut-off excludes general annotations such as: metabolic process, single-organism process or localisation. The cut-off can be chosen from one of provided: 1e-5 , 0.01 or 0.1 or be defined by user. To define your own cut-off, enter your cut-off in empty box next to cut-offs and press ENTER. The table will be updated. The functional annotations are derived from Gene Ontology project.

The functional annotations of binding partner can be used to filter instances in dataset to limit instances to these which share the same function with binding partner.

Steps
  1. Define the binding partner in the input box.
  2. Click search button to see functional annotations of binding partner.
  3. Select the functional annotations which you want to use as filters from the table.
  4. Click Filter button to view instances which share the same annotations or Add button to save filter.

Step 1. The binding partner can be provided as UniProt protein accession or protein name. If you start typing the protein name, the list of possible proteins will show below the box. Click on protein of your choice from the list to define the binding partner.

Filtering
Filtering.
  1. Defined binding partner.
  2. Change cut-off (optional).
  3. Select the annotations from table
  4. Click Filter button or Add button to save filter.

Interactors

Interacting proteins of binding partner are provided with information how likely a given interactor is shared by any two proteins in the proteome. The probabilities are computed based on UniRef50 clusters (Sig (UniRef50) column) and without any clustering (Sig (NoClustering) column). The user can limit the number of returned interactors to these more specific by setting cut-off to lower score. The cut-off can be chosen from one of provided: 1e-5, 0.01 or 0.1 or be defined by user. To define your own cut-off, enter your cut-off in empty box next to cut-offs and press ENTER. The table will be updated.

The interactors of binding partner can be used to limit instances to these which occur in interacting proteins of binding partner and interact with the binding partner.

Steps
  1. Define the binding partner in the input box.
  2. Click search button to see interactors of binding partner.
  3. Select the interacting proteins which you want to use as filters from the table.
  4. Click Filter button to view instances which occur in interacting proteins of binding partner and interact with defined binding partner or click Add button to save filter.

Step 1. The binding partner can be provided as UniProt protein accession or protein name. If you start typing the protein name, the list of possible proteins will show below the box. Click on protein of your choice from the list to define the binding partner.

Filtering
Filtering.
  1. Defined binding partner.
  2. Change cut-off (optional).
  3. Select interactors from table
  4. Click Filter button or Add button to save filter.

Hub domain

Interacting domains can be used to limit instances to these which could interact with specified binding domains, i.e. domains which occur in known interacting proteins for a given instance.

Steps
  1. Search for domains using input box.
  2. Select the interacting domain(s) which you want to use as filters from the table.
  3. Click Filter button to view instances which interact with selected binding domains, or click Add button if you want to add this filter and specify another one.

Step 1. Search for domains. Start typing domain name or shortcode in the input box and possible domains will show in the table below. The table will be updated automatically whenever you start typing in the input box.

Filtering
Filtering.
  1. Search for domains.
  2. Choose domain(s) from the table.
  3. Click Filter button to filter instances or Add button to save filter options.

Annotation

The instances can be filtered based on possible localisation or ontology and interaction annotations for motif set.

Localisation

The protein cellular component annotations can be used to limit number of instances occurring in (or outside) specific localisations. All possible subcellular localisations for motif instances in dataset are listed in table and each annotation is provided with information how many instances occur in specific cellular component (# column).

Steps
  1. Select the localisation(s) from table.
  2. Click on Filter in button to view instances which occur in defined localisations or click on Filter out button to view instances which occur outside defined localisations. Click one of Add buttons to save filter.

The table can be searched by using search box above the table. Start typing the localisation and the table will be updated automatically.

Filtering
Filtering.
  1. Search table (optional).
  2. Select localisation(s).
  3. lick one of Filter buttons to filter instances or one of Add button to save filter.

Function

The ontology and interaction terms can be used to filter the motif instances which are assigned to selected terms by user. All possible functional annotations for instances in motif set are listed in the tables. Each term is provided with enrichment scores and significance from enrichment analysis.

Steps
  1. Select the term(s) from the table.
  2. Click on Filter button to view instances which are mapped to selected terms, or Add button to save filter.

The same filtering can be performed when you are on Function page.

Filtering
  1. Search table (optional).
  2. Select annotation(s).
  3. lick one of Filter buttons to filter instances or one of Add button to save filter.

Evolution

Taxonomic range can be used to limit number of instances to these conserved outside (or inside) specific clad or species. All possible clads (and species) are listed in the table.

Steps
  1. Specify the alignment.
  2. Specify if you want to filter instances based on conservation inside or outside selected species or clad.
  3. Specify the species/clad to be used as filter by clicking on one from the table.
  4. Click Filter button to view instances which are conserved inside or outside selected species or clad, or Add button to save filter.

The table with taxonomic range can be searched by using search box above the table. Start typing the species or clad name and the table will be updated automatically.

Filtering
Filtering.
  1. Choose alignment.
  2. Specify if you want filter instances based on conservation inside or outside species.
  3. Search table (optional).
  4. Select species/clade from table.
  5. Click on Filter button, or Add button to save filter.

Accessions

There are two options to filter consensus matches based on provided accessions. The instances can be filtered by protein accessions or ontology and interaction identifiers.

Protein accession

UniProt protein accessions can be used to limit number of instances to these occurring in specific proteins.

Steps
  1. Enter the UniProt protein accession separated by ENTER in the input box.
  2. Click on Filter button to view instances which occur in provided proteins, or Add button to save filter.

UniProt protein accessions are 6-10 alphanumerical stable identifiers. Examples of UniProt protein accessions in human:

UniProt accession Protein Name
P04637 Cellular tumor antigen p53
P11532 Dystrophin
Q8WZ42 Titin
Filtering
Filtering.
  1. Enter UniProt protein accessions.
  2. Click on Filter button, or Add button to save filter.

Annotation identifiers

Several annotations such as: Gene Ontology, UniProt Keywords, Pfam and UniProt accessions can be used to limit number of motif instances in dataset. Gene Ontology and UniProt Keywords filter instances by function and localisation, and Pfam identifiers and UniProt accessions filter instances based on interaction data. Provided UniProt accession(s) indicate binding partner(s) i.e. interacting proteins, and Pfam id(s) describe interacting domain(s) i.e. domains occurring in interacting proteins.

Steps
  1. Enter accessions separated by ENTER in the input box.
  2. Click on Filter button to view filtered instances assigned to provided annotations, or Add button to save filter.

Examples of accessions:

Source Accession Name
Gene Ontology GO:0007049 Cell cycle
UniProt keyword KW-0498 Mitosis
Pfam domain PF00017 SH2 domain
UniProt protein P04637 Cellular tumor antigen p53 (H.sapiens)
Filtering
Filtering.
  1. Enter accessions.
  2. Click on Filter button, or Add button to save filter.

Accessibility

Accessibility information can be used to limit number of instances to these which are accessible to intracellular proteins. Motif instances are provided with warnings which indicate that instance is inaccessible to intracellular proteins. These warnings can be used to filter instances.

Steps
  1. Switch on/off warning(s) from table. If warning is switched off, then instances with that warning will be excluded from results.
  2. Click on Filter button to filter instances, or Add button to save filter.

The same filtering can be done on Instance page by clicking on above the right table corner.

Filtering
Filtering.
  1. Switch on/off warning type.
  2. Click on Filter button, or Add button to save filter.

Shared annotations

Shared annotations data provided by user on input page can be used to filter motif instances. The results can be limited to these instances which are known to interact with defined set of proteins, or these instances which share at least one GO term with defined set of proteins.

Steps
  1. Switch on/off annotations from table. If annotation is switched on, then instances without shared annotation will be excluded from results.
  2. Click on Filter button to filter instances, or Add button to save filter.

The same filtering can be done on Instance page by clicking on above the right table corner.

Filtering
Filtering.
  1. Switch on/off annotation type.
  2. Click on Filter button, or Add button to save filter.

Retrieve old job

The user can retrieve previous searches using a unique identifier - JobID. JobID can be found on Instances page in the right top corner. Jobs are stored for two weeks.

Data sources

Databases

name description PMID URL
UniProt Protein accessions, names, sequences, families, UniRef clusters and feature annotations. 25348405 http://www.uniprot.org
ELM Manually curated linear motifs. 26615199 http://elm.eu.org
Pfam Functional regions and binding domains. 24288371 http://pfam.xfam.org
Phospho.ELM Experimentally verified phosphorylation sites. 21062810 http://phospho.elm.eu.org
PhosphoSitePlus Phosphorylation, ubiquitination, acetylation and methylation sites. 22135298 http://www.phosphosite.org/homeAction.do
PDB Experimentally resolved protein tertiary structures. 10592235 http://www.rcsb.org/pdb/home/home.do
DSSP Secondary structure derived from PDB tertiary structures. 25352545 http://swift.cmbi.ru.nl/gv/dssp/
dbSNP Single-nucleotide polymorphism. NCBI Handbook [Internet]. Chapter 5. http://www.ncbi.nlm.nih.gov/SNP
1000genomes Single-nucleotide polymorphism. 23128226 http://www.1000genomes.org
switches.ELM Experimentally validated motif-based molecular switches. 23550212 http://switches.elm.eu.org
Gene Ontology Gene ontology annotations. 25428369 http://geneontology.org
IntAct Experimentally validated protein-protein interactions. 24234451 http://www.ebi.ac.uk/intact/
HIPPIE Validated human protein-protein interactions. 27794551 http://cbdm-01.zdv.uni-mainz.de/~mschaefer/hippie/

Programs

name description PMID URL
IUPred Intrinsically disordered regions. 15769473 http://iupred.enzim.hu
SLiMPrints Conservation of residues across the alignment. 22977176 http://bioware.ucd.ie
Anchor Binding sites in disordered regions. 19412530 http://anchor.enzim.hu