GRAMM: Docking Web Server


This is the Web interface to our protein docking software GRAMM (Global RAnge Molecular Matching). GRAMM systematically maps the intermolecular energy landscape by predicting a spectrum of docking poses corresponding to stable (deep energy minima) and transient (shallow minima) protein interactions. More information on the GRAMM methodology is on our laboratory website.




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.

Questions:

Send questions or comments to gramm@ku.edu.

References

GRAMM web-server should be cited as:

Singh, A., Copeland, M.M., Kundrotas, P.J., Vakser, I.A., 2024, GRAMM Web Server for Protein Docking, Methods in Mol. Biol., 2714:101-112.

Other GRAMM docking references:

Singh A., Dauzhenka T., Kundrotas P.J., Sternberg M.J.E., Vakser I.A.. 2020, Application of docking methodologies to modeled proteins, Proteins, 88:1180–88.

Tovchigrechko, A., Vakser, I.A., 2006, GRAMM-X public web server for protein–protein docking, Nucleic Acids Research, 34:W310–W314.

Vakser, I.A., 1996, Long-distance potentials: An approach to the multiple-minima problem in ligand-receptor interaction, Protein Eng., 9:37-41.

Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A.A., Aflalo, C., Vakser, I.A., 1992, Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques, Proc. Natl. Acad. Sci. USA, 89:2195-2199.