vsFilt: a tool to improve virtual screening by structural filtration of docking poses

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Choose input mode

Submit a new task

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

Submit docked ligand poses, protein structure, and the interaction profile or access a previous submission by TaskID

Claim your results by TaskID

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:

Docked ligand poses

Upload the docked ligand poses

Choose a file…

Upload a file with docked ligand poses in SDF format. File size must not exceed 500 MB. File extention must be "sdf" for plain text format or "tgz" for a TAR-GZ archive . E.g.: library.sdf or library.tgz.

Protein 3D-model

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.: protein.pdb.

Security and sharing

Service code: Administrative use only

Restrict access to task files by IP address:

No Yes

Restrict 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

vsFilt protein-ligand interaction profile

Provide the interaction profile:

Create and edit on-site Upload as a text file

Ligand	Protein			# of interactions	Action

funcional group	resname	resnum	chain

Add at least one filtering rule

Paste/create/edit your interaction profile (at most 5000 characters)

Additional vsFilt constraints for H-bonds

Apply angle constraints for h-bonds: No Yes

Apply tight constraints for h-bonds: No Yes