MFDp2 - Help and tutorial

This page explains how to perform predictions using MFDp and how to obtain and analyse the results.

HINT: The symbols indicate availability of (additional) explanations. Clicking opens a new window with help and hints related to the selected section/task.


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Introduction

The MFDp2 web server is designed for protein disorder prediction.

Results will be stored online for at least 3 months, and are accessible through direct link provided after protein submission, and sent by e-mail after results are ready.

MFDp2 combines per-residue disorder probabilities predicted by MFDp with per-sequence disorder content predicted by DisCon, and applies novel post-processing filters to provide disorder predictions with improved predictive quality. It outputs optimized per-residue disorder probability profiles, per-sequence disorder content, list (with analysis) of disordered segments, and several profiles that help in the interpretation of the results. The results are available online in graphical format and can be also downloaded in text-based (parsable) format.

To use the MFDp2 webserver, a three easy steps should be followed:

  1. Copy and paste protein sequences list in FASTA format into text field or upload fasta formatted file (an "Example" button may be used to see an example input of the FASTA format).

  2. Provide e-mail address (optional). If e-mail is provided a notification e-mail will be sent once the results are ready. The notification will include a web address where the results are stored.

  3. Click "Run MFDp2" button to start the predictions.

Next, the request will be added to our processing queue which in executed in the order in which the requests were received. Notification will be displayed on the screen once the request will be processed. Once the predictions are ready the link to the results page will be provided (the same link will be sent in email). This page displays detailed results which are explained below. Please save this link for future reference.


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Results page

This page provides overview of predictions made by MFDp2 webserver for all submitted proteins (see area marked by red number 1 in the picture below), and allows to download predictions (2) as .csv or .fasta file. To see more detailed predictions for a given protein its name or sequence should be clicked(3). This action opens the protein's detailed results page.

The Results page includes brief disorder statistics followed by per-residue disorder prediction for each submitted protein. GREEN letters represent residues predicted as ordered and RED letters correspond to the predicted disordered residues. The proteins are also color coded based on their disorder content, green border indicates proteins with low disorder content, whereas red border indicates protein with high disorder content.

By clicking on protein's name or sequence a page with detailed information about the disorder prediction is opened.


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Downloading the results

The results can be downloaded as .csv (see area marked by red number 1 in the picture below) or .fasta (2) file. The file will always contain protein sequence and MFDp2 predictions (both per-residue probabilities and binary predictions). Additional information predicted by other methods may be included, by selecting corresponding checkboxes. The MFDp2 server includes outputs of PSIPred (predicted Secondary Structure (SS)) (3), Real-SPINE3 (predicted Relative Solvent Accessibility (RSA)) (4), MFDp (predicted disorder) (5), and DisCon (predicted disorder content) (6).

In .csv file each line starts with a user-given protein name, the type of information that the line provides and the information. These three fields are comma separated. Example .csv file follows:

DP00582,AA Sequence,Q,D,K,C,K,K,V,Y,E,...
DP00582,MFDp2 probabilities,0.499,0.499,0.466,0.435,0.408,0.386,0.366,0.348,0.331,...
DP00582,MFDp2 binary,0,0,0,0,0,0,0,0,0,...

Each .fasta file starts with a header that identifies format of the subsequent data, and then the data is outputted for each protein. Example of .fasta file:

#File format:
#>Protein name
#AA Sequence
#MFDp2 probabilities - separated by comma
#MFDp2 binary
>DP00582
QDKCKKVYE...
0.499,0.499,0.466,0.435,0.408,0.386,0.366,0.348,0.331,...
000000000...


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Detailed results page

This page provides more detailed information about predicted disorder for a given protein (see area marked by red number 1 in the picture below). It also provides comprehensive information that allows to profile disorder (2). The profile includes conveniently visualized information concerning residue conservation, predicted secondary structure, relative solvent accessibility, disorder profiles, and flexibility. The profile is color coded to ease the interpretation. Values of the abovementioned characteristics (conservation, secondary structure, etc.) which are associated with disordered residues are shown in red while values associated with order are shown in green. This page also contains a list of predicted disorder segments along with basic statistics (3).


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Protein's disorder info

This section provides an overview of predicted disorder statistics, and per residue binary predictions. GREEN letters represent residues predicted as ordered, and RED letters correspond to predicted disordered residues. All disorder segments are links to the Segment section which provides certain characteristic features/profile of individual disordered segments in more detail.


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Per-residue disorder profiles

MFDp2 generates detailed per-residue graphs as a part of detailed per-protein results. This graph presents predicted per-residue disorder probability along with information about important input features that form disorder profile. Features are color coded according to their correlation with disorder. The more red the feature is the more likely the corresponding residue is to be in disordered state, whereas the greener the more likely that this residue will be ordered. The profile includes the following information:

The above values included in the profile correspond to "strong" predictive inputs used by the MFDp2 webserver.


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Disorder segments

This section of detailed per-protein results lists all predicted disorder segments and includes links to the more detailed descriptions of the segments (see area marked by red number 1 in the picture below). It also shows a basic statistics including length and position of the segment in the sequence.


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