pocketZebra: New task

Version 2.0

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Choose input mode

Mode 1: Submit a multiple sequence alignment of a protein family/superfamily and a 3D-structure of the representative protein

Mode 2: Submit a Zebra bioinformatic analysis file and a 3D-structure of the representative protein

Claim your results by TaskID (access the results and progress log of a previously submitted task)

Submit a multiple protein alignment and a representative protein structure as a new task, or access a previous submission by TaskID

Claim your results by TaskID

TaskID:

Enter TaskID (a 14-symbol code XXXXXXXXXXXXXXX) which was assiged to a previously submitted task and press "Claim". You will be redirected to the progress log page.

Submit a new task

Show tips on how to use pocketZebra

General input to Zebra

To use Zebra you have to submit (1) a multiple alignment of proteins in the FASTA format and (2) a representative protein (i.e., the query) structure in the PDB format which should correspond to one of the proteins in the multiple alignment. This input can be prepared automatically based on your query protein by the Mustguseal web-server via a web-interface (see below).

Bioinformatic analysis using Zebra and Mustguseal in four simple steps
(click here for an illustrated guide)

Step 1: Choose the query protein. Choose the query protein based on your particular task and primary interest. It can be the target protein selected for the further experimental design, the most studied member of the superfamily, or a protein which you are the most familiar with.

Step 2: Automatically construct a large alignment of diverse protein families. Press the "Mustguseal in NOW" button in the "The multiple protein alignment" box below. This will redirect you to the Mustguseal web-server and load a preselected set of parameters (i.e., the Scenario 2). Mustguseal can automatically construct large structure-based sequence alignments of thousands of proteins based on all available information about their structures and sequences in public databases. Enter the PDB ID and chain ID of your query protein in the "Query protein" box and press "Submit" to automatically construct a large structure-guided sequence alignment of proteins with high structural but low sequence similarity to your query protein.

Step 3: Automatically transfer your data from Mustguseal to Zebra. At the Mustguseal's "Results" page scroll down and press the "Submit to Zebra2" button. This will automatically transfer the collected sequence and structural data to Zebra.

Step 4: Start Zebra. Press "Submit" button to start the Zebra routine. When your task is processed, press "Results" to access the results and the download section, and press "Analysis" to load the interactive on-line analysis tools.

Useful links:

The complete guide to Zebra is provided at the main page
Notes on preparing the input data
The Zebra parameters
The Zebra output
The Zebra examples
The Zebra file sharing and security features
Citing the Zebra server

Hidden input mode selector If you see this message and an input field above, please report the bug to administrator

The multiple protein alignment

Upload the multiple protein alignment file

Choose a file…

Upload a file with a multiple protein alignment in fasta format. File size must not exceed 100 MB. File extention must be "fasta" or "fasta_aln". E.g.: file.fasta_aln.

No alignment? Press to run the Mustguseal web-server with a pre-selected set of parameters and automatically construct a multiple alignment of your protein families for further analysis by the pocketZebra.

Remote link to file

Remote links to the Mustguseal server only are accepted

The Zebra bioinformatic analysis

Upload the Zebra bioinformatic analysis file

Choose a file…

Upload a Zebra bioinformatic analysis file in proprietary format. File size must not exceed 100 MB. File extention must be "ze". E.g.: zebra.ze.

The representative protein structure

Upload the protein structure file

Choose a file…

Upload a file with protein structure in the PDB format. File size must not exceed 10 MB. File extention must be "pdb". E.g.: filename.pdb.

Remote link to file

Remote links to the Mustguseal server only are accepted

Select a protein chain Enter a case sensitive chain ID (e.g., 'A' to select chain A) or 'first' to select the first chain in the uploaded file.

Set the ID of the representative protein in the multiple alignment Enter a positive integer (e.g., '10' to select the 10-th protein in the alignment to match the protein structure) or 'auto' to select the best match automatically

Security and sharing

Service code: Administrative use only

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Allow access to task files by IP address:

No Yes

Allow access to task files by password:

No Yes

Enter a string of letters and numbers at least 6 symbols long Enter the same password again

Zebra options: general

Select columns in the multiple sequence alignment:

Consider all columns
Select columns by residues around a ligand in PDB
Select columns by column ID

Consider only residues within radius from ligand in PDB

Chain:

Resname:

Resid:

Radius:

E.g., enter 'A', 'SOX', '55', and '5.5' into the respective fields to select all residues within 5.5 Angstroms from ligand A:SOX:55 in the representative protein 3D-structure)

Consider only residues defined by columnID Enter a set of comma-separated integers (e.g., '1,12,25,67,100' to select the corresponding columns in the alignment; the numbering starts from '1', at most 999 characters)

Max content of gaps allowed on a column (%)

Enter an integer (e.g., '5' to set the threshold to 5% from the total number of proteins in the alignment)

Zebra options: statistical significance

Number of random shuffles for each column

Enter an integer ≤10000 (e.g., '1000' to shuffle each column 1000 times)

Zebra options: 3D-mode

Radius in Angstroms for neighbor selection

Enter a floating-point number (e.g., '4' to select all neighbors within 4 Angstroms or '0' to deactivate)

Zebra options: classification into subfamilies

Classify proteins into subfamilies:

Zebra CD-HIT Manual

Min number of subfamilies in a classification Enter an integer (e.g., '5' to consider classifications with at least 5 subfamilies) or 'auto' for automatic

Max number of subfamilies in a classification Enter an integer (e.g., '10' to consider classifications with at most 10 subfamilies) or 'auto' for automatic

Max amount of outliers in a classification (%) Enter an integer within a range [0; 100) (e.g., '20' to consider classifications with at most 20% outliers from the total number of proteins in the multiple alignment)

Min size of a subfamily (%) Enter an integer within a range [0; 50] (e.g., '5' to consider only subfamilies with at least 5% proteins from the total number of proteins in the multiple alignment, or '0' to consider all subfamilies with at least 3 proteins)

Sequence identity threshold (%) Enter an integer within a range [10; 100] (e.g., '95' to set the threshold to 95%)

Upload the classification file

Choose a file…

Upload a file with a manual assignment of proteins to subfamilies. File size must not exceed 10 MB. File extention must be "txt" or "groupfile". E.g.: file.txt or file.groupfile.

Pockets options: detection

Select pocket detection method:

Fpocket 2.0 Auto Fpocket 2.0 Manual Manual

Fpocket 2.0 instructions Enter command line text instructions for Fpocket 2.0 (e.g., '-i 27' to set 'Minimum number of a-sphere per pocket' to 27)

Upload the pocket definition file

Choose a file…

Upload file with manual assignment of atoms/residues to pockets. File size must not exceed 10 MB. File extention must be "txt". E.g.: pockets.txt

Pockets options: statistical significance and ranking

Selection of subfamily-specific positions:

By global P-value minimum By Z-score cut-off

Z-score threshold Enter a float (e.g., 0.5 to consider only positions with Z-scores at least that large)