Yosshi: New task

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Dear User. We appreciate your interest in the Yosshi. This service will be closed for maintenance starting from ... and until ... Please plan your research activities involving this service accordingly. You can contact Support with urgent requests.

Choose input mode

Submit a new task

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

General input to Yosshi

To use Yosshi 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).

Disulfide engineering of your protein using Yosshi 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 3). 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 Yosshi. At the Mustguseal's "Results" page scroll down and press the "Submit to Yosshi" button. This will automatically transfer the collected sequence and structural data to Yosshi.

Step 4: Start Yosshi. Press "Submit" button to start the Yosshi 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 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 Yosshi.

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.
If your protein has multiple chains and you want to search for inter-chain S-S bonds, see this tutorial.

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

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

Yosshi options: First tier filter

Set the cut-off distance between CA-CA atoms of two residues

Enter a floating-point number (e.g., '5.5' to set the cut-off to 5.5 angstroms)

Set the cut-off distance between CB-CB atoms of two residues excl. Gly Enter a floating-point number (e.g., '5.5' to set the cut-off to 5.5 angstroms)

Yosshi options: bioinformatic analysis

Set the alignment window size

Enter an integer betwee 0 and 3

Yosshi options: 3D-motif analysis

Select the mode to run the 3D-motif analysis:

Flexible Rigid Custom Off

Select the 3D-motif library:

Core collection Complete collection

Set the RMSD mean value Enter a floating-point number (e.g., '0.5' to set the value to 0.5 angstrom)

Set the RMSD standard deviation value Enter a floating-point number (e.g., '0.2' to set the value to 0.2 angstroms)

Set the statistical significance p-value Enter a floating-point number (e.g., '0.05' to set the value to 5%)

Yosshi options: output

Provide HTML links to PDB, UniProt, and BacDive:

No Yes

Yosshi: your web-server for S-S bond harvesting in protein superfamilies

Version 1.1

Attention!

Dear User. We appreciate your interest in the Yosshi. This service will be closed for maintenance starting from ... and until ... Please plan your research activities involving this service accordingly. You can contact Support with urgent requests.

Choose input mode

Claim your results by TaskID

Submit a new task

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 Yosshi.