Vakser Lab

GRAMM-X Protein-Protein Docking Web Server v.1.2.0

This is the Web interface to our current protein docking software made available to the public. This software is different from the original GRAMM, except that both packages use FFT for the global search of the best rigid body conformations.
Note: This server will ignore any small ligands or other non-protein molecules in the input files. It is designed exclusively for docking pairs of protein molecules.

You can submit input files and parameters to this web server and the docking
simulation will be run on our computer cluster.

When the results are ready, they will be saved in a temporary directory on the web server and the link to that directory will be sent to you. Please, cite the References if you use in a publication the results obtained from this server.

Please, read the Conditions of Use before proceeding.

Questions

Send questions or comments to Andrey Tovchigrechko.

Start new GRAMM-X simulation

Main Input

Receptor protein PDB file (Required)

Select the PDB file on your computer to use as the receptor. This file will be uploaded to our server.

Chain Ids of the Receptor

Specify chain id's for the receptor as one or several letters. Examples: LH - chains L and H; C - chain C; leaving this field empty will mean to use all chains from the receptor file.

Ligand protein PDB file (Required)

Select the PDB file on your computer to use as the ligand. This file will be uploaded to our server.

Chain Ids of the Ligand

Specify chain id's for the ligand as one or several letters. Examples: AB - chains A and B; X - chain X; leaving this field empty will mean to use all chains from the ligand file.

Email address to receive results. (Required)

When your simulation is done, the link to the results will be sent to this
email address.

Optional Parameters

Number of models to output

Specify the number of models (alternative predictions) to save in the final output file (from 1 to 300).

Interface residue constraints (Click here for Help)

Potential receptor interface residues

Receptor residues that might form the interface with the ligand. Example: 15-23:L,35:H,78:H will select receptor residues from 15 to 23 in chain L and residues 35 and 78 in chain H. See Help for details.

Receptor residues required

Number of receptor residues from the potential interface list that are required to be in contact with some residue of the ligand. Enter all for all potential interface residues of the receptor.

Potential ligand interface residues

Ligand residues that might form the interface with the receptor. Example: 1-43: will select ligand residues from 1 to 43 from a chain with an empty chain Id. See Help for details

Ligand residues required

Number of ligand residues from the potential interface list that are required to be in contact with some residue of the receptor. Enter all for all potential interface residues of the ligand.

Receptor-ligand residue pairs required

Number of receptor-ligand residue pairs from the lists of the potential interface residues that are required to be in contact with each other.

Number of identical monomers if this complex is a homo-multimer

If your complex is a symmetrical homo-multimer, then we will try to build it from this number of identical subunits specified as the receptor. Leave blank if this is not a homo-multimer. Currently the only other supported value is 2 (for homo-dimers).

References

Tovchigrechko A, Vakser IA. GRAMM-X public web server for protein-protein docking. Nucleic Acids Res. 2006; 34:W310-4.
Tovchigrechko A, Vakser IA. Development and testing of an automated approach to protein docking. Proteins 2005;60(2):296-301.
As part of its docking protocol, GRAMM-X incorporates a new improved version of the original GRAMM global search algorithm. The description of the original algorithm and its applications can be found in references on the GRAMM v.1 page.

Conditions of Use

This computationally intensive service is provided to the research community free of charge utilizing our computational resources, which are limited.

To ensure the fair use of this server, we ask that no person submits more than ten simulation requests per day. We reserve the right to block access from those not honoring this request or involved in any other misuse of this service.

The simulation requests will be queued and the wait time will vary depending on the load of our cluster.

Disclaimer: This is research software under active development, and we make no guarantees regarding the accuracy of its predictions. The results of simulations are provided AS IS, and should be used at your own risk. We do not warrant or assume any liability or responsibility for the accuracy, completeness, or usefulness of any information provided on this server.

Sections

Personal tools

GRAMM-X Protein-Protein Docking Web Server v.1.2.0

Questions

Start new GRAMM-X simulation

References

Conditions of Use