DOCK Blaster:FAQ

DOCK Blaster FAQ

Q1. What is DOCK Blaster?

DOCK Blaster is a free web-based service for molecular docking and virtual screening. It uses UCSF DOCK 3.5.54 as a docking engine, and ZINC as a dockable database. It runs entirely on our 400 CPU cluster in our Mission Bay laboratories in San Francisco. The graphical user interface comprises an expert system that is designed to help you get useful results. We aim to publish a paper in 2007.

Q2. How do I use DOCK Blaster?

You need a structure of your target, and an indication of the binding site for which you want to find a small molecule ligand. The target should be in PDB format, and must conform to certain rules (see Preparing Input. The indicatation of the binding site is ideally a docked ligand in mol2 format, but could also be residues surrounding the binding site in PDB format. Point your browser to blaster.docking.org, enter your data, and click "I agree, DOCK!".

Q3. How much does DOCK Blaster cost to use?

DOCK Blaster is free to everyone. It is supported by NIH grant GM71896 (to BKS and JJI).

Q4. I'm having trouble using DOCK Blaster

We anticipate several sorts of problems:

• 1. The entire site is broken or seems to be behaving incorrectly.

If so, please write to support at docking.org, describing the problem, so we can fix it.

• 2. You cannot get a job to start, because DOCK Blaster complains about your input during the Scrutinizer step.

We know this can be frustrating. We have tried to make the error messages helpful, descriptive and short. Please attempt to follow them. However, if you are not making progress after you have tried 5 times to correct your input, please email support at docking.org, including your JOB ID number if available, so that we can look at the problem.

• 3. Your job gets queued, but does not get started.

Solution: our cluster may be very busy. Please check back again tomorrow.

• 4. Your job fails or seems to get stuck during "Target Preparation".

Solution:

• 5. Your job fails or seems to get stuck during "Calibration".
• 6. You get to "Calibration Done", but you don't know what to do next.

Solution:

• 7. You cannot start a docking job.

Solution:

• 8. Your queued docking job will not start.

Solution: your cluster may be very busy. Please check back again tomorrow.

• 9. Your job fails or seems to get stuck during "Docking".

Solution:

• 10. You get to the "Results" stage, but you don't know what to do.

Solution:

• 11. You are having trouble with Jmol/Java, Chimera, PyMol.

Solution:

• 12. You have exhausted your quota of allowed jobs for the day.

Solution: please come back tomorrow and try again, or write us at support at docking.org stating why you think you should have a higher quota.

• 13. You ran your job 14 days ago and it has vanished from the system.

Solution: 14.

Q5. Can I trust DOCK Blaster?

You are wise to be cautious about trusting the results produced by DOCK Blaster. Molecular docking and virtual screening methods are notoriously succeptible to many possible failures due to the numerous approximations made in the calculations. We recognize this inherent skepticism, and have therefore attempted to provide tools with which you can reassure yourself that DOCK Blaster results really are worth investigating - or not, as the case may be.

Here is the evidence we will gather to investigate the calculation:

• 1. score of the supplier ligand in its supplied pose
• 2. ability to re-dock the supplied ligand
• 3. score & pose of similar ligands, drawn from ZINC
• 4. score & pose of property-matched, dissimilar ligands drawn from ZINC
• 5. score of extrema ligands
• 6. score of actives, if supplied
• 7. score of inactives, if supplied
• 8. appearance of top scoring ligands from the lead-like or fragment-like database.

Now, we review how to evaluate the above results in order to estimate whether the results are worth pursuing, for example, by purchasing compounds.

Q6. I think DOCK Blaster has crashed on my job

Normally, DOCK Blaster should recover from a crash, and do two things:

• 1. inform the site manager that a crash occurred.
• 2. email the originator of the job, if an email address was supplied.

Sometimes this email may not be sent for up to 3 hours after a crash. It is possible that the email sending itself fails.

If you believe your job has crashed, we suggest one of two actions, depending on the nature of the crash.

• 1. If you believe the job crashed due to a general system failure, and not due to your calculation itself, then we recommend trying to re-run the job before contacting DOCK Blaster support. If you try again, and the job crashes at the same or similar point, then please write to support at docking.org to inform us of this so we can investigate.
• 2. If you believe the job crashed due to causes specific to your calculation, then please write support at docking.org right away, telling us any relevant information you think we should know.

Q7. I have privacy concerns about my data

DOCK Blaster is a free public service, run on taxpayer-supported computers. We do not support private calculations. All calculations

Q99. I have a question that isn't listed here...

When does this awesome idea become reality?