DOCK Blaster:Timings

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DOCK Blaster is a pipeline with several steps. The time each step takes will depend on the target, any ligands you supply, and of course competition from other users for the CPU cluster. Here we take up the time for each of the major steps.

Preparer

Here most of the time is your own, as you prepare the files required to run DOCK Blaster. When you click "DOCK!", you launch the scrutinizer.

Typical time: entirely up to you.

Scrutinizer

This step checks your input, and attempts to rapidly reject insufficient or incorrectly formatted data as quickly as possible so that you can try again. We estimate that 80% of the time a user clicks "DOCK!" in the Preparer, the Scrutinizer will return within 30 seconds rejecting the input and giving reasons for why the rejection was made.

Typical time: 30 seconds from "DOCK!" to either "Job queued" or "Job rejected, because..."

Calibration

This step attempts to calibrate the docking model by test-docking a small number of molecules using two different sampling schemes and two different scoring schemes. The goal is to decide which of the four conditions is best for database docking (next step).

The time this step depends on the number of ligands you may have supplied as actives or inactives. The quickest this step can be is about 8 minutes. We have seen cases where it takes 24 hours - under admittedly extreme circumstances.

We expect that typical times for calibration will be in the range of 10-30 minutes. The goal is to give you feedback quickly so that you can evaluate whether docking is likely to be able to work successfully for this project.

Docking

Once you have reviewed the results of calibration and picked the sampling and scoring conditions you think are best for full scale docking, you are free to dock a database. Again here the time taken depends hugely on both the characteristics of the binding site and the number and size of molecules in the database to dock.

Minimum time: allow 1hr. Typical time: 24 hrs. Extreme conditions: 7 days (but we'll be in touch if this happens more than once or twice!)

Results browsing

Once the results are ready, all you are doing is loading pages and browsing results. Loading a page of 500 results into the browser could take a minute, but will often be less. Downloading files into Chimera or PyMol could take a couple of minutes, and will depend on the speed of your internet connection, and whether there are any bottlenecks between your site and UCSF.

Typical time: most operations should complete in under 1 minute. If it takes much longer, there may be a problem.