UNRES-Dock utilizes multiplexed replica exchange MD simulation (MREMD) with 24 random starting structures of a complex, with diverse orientations of monomers. The monomers are placed to interact weakly with each other, the smallest periodic-box size prohibiting interactions between a molecule with its image is estimated. A set of log-Gaussian restraints are imposed on both monomers for protein-protein docking, and only on the first chain for protein-peptide docking.
Use the "Save & submit" button to start calculations.
Use the "Refresh" button to check the status of a simulation:
After the server job has been submitted the "waiting in the queue to start" message will be displayed in the status field, which will subsequently change to "running", "postprocessing", and "done". While the job has the "running" status, the percentage of job accomplishment is displayed. It should be noted that the "100%" accomplishment refers to the production phase of a job, after which the postprocessing phase is triggered which also takes some time and whose progress is not monitored. The page is autorefreshed every 30 sec.
Any single job can be accessed later (for
at least 14 days) using the address of the web page displayed after job
Registered users can save all their jobs and access them later after logging in. Note that the results will be available for a limited period of time, depending on the storage space availability (at least 30 days).