DOCK Blaster:FAQ

DOCK Blaster is a free virtual screening service. These are the frequently asked questions. Questions that take more than a couple of lines may get their own wiki article.

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 guide both novices and experts to useful results. An academic paper about DOCK Blaster will be published soon.

Why DOCK Blaster? Docking programs have been around for ages. What's new?

We are attempting to serve a constituency of investigators who would like to use docking for their projects but find the barriers to setting up their own computational lab prevent them from doing so. Experts are still welcome to use DOCK Blaster, of course. But we are really aiming to serve a broad community of biologists who seek new chemistry for their biological targets.

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 [1] to get started.

How much does DOCK Blaster cost to use?

DOCK Blaster is free for everyone. It is supported by NIH grant GM71896 (to BKS and JJI). We reserve the right to limit usage, particularly by intensive users.

I'm having trouble using DOCK Blaster

Please see the Problems page for a general overview of all problems. Please see the Bugs page for information about bugs. Please report bugs, as completely as possible, to support at docking.org.

Preparer/Scrutinizer Problems

There are many reasons why your input may be rejected by the DOCK Blaster:scrutinizer. Many of these owe to the nature of the file formats we accept (PDB, mol2) and the complexity of protein binding sites. We know this can be frustrating. We have tried to make the error messages helpful, descriptive and short. Please read them carefully and attempt to follow them. However, if you are not making progress after you have tried five times to correct your input, please email support at docking.org, including your JOB ID number if available, and a short description of the problem as you see it, so that we can look at the problem.

Target Preparation / Calibration Problems

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

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

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

Solution:

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

Solution:

• 6. You get to "Calibration Done", but you don't know what to do next.

Solution:

Docking Stage Problems

• You cannot start a docking job.

Solution:

• Your queued docking job does not start.

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

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

Solution:

• You want to dock a database that is not available.

Solution:

Results Browser Problems

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

Solution:

• You are having trouble with applets or helper applications such as Jmol/Java, Chimera, PyMol.

Solution:

• 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.

• You ran your job 28 days ago and it has vanished from the system.

Solution: We purge data that has been dormant for 28 days. Please visit and "touch" your job to have it retained for 28 more days.

Can I trust DOCK Blaster?

This question warrants its own article. DOCK Blaster:Reliability

I think DOCK Blaster has crashed on my job

"Crashing" here can refer to two things.

• 1. PIPELINE ERROR. A program in the DOCK Blaster pipeline terminated abnormally, perhaps because it was unable to handle the input it was given. This can be handled in one of two ways. Ideally, the job will stop and an intelligible error message will be produced which can guide the user to modifying the input. The system manager will also be informed, as the problem may reflect a "bug" in the software. Sometimes the job may stop without producing a message of any kind.

• 2. PLATFORM ERROR. A job stops because the computer it was running on crashed, or there was some other system-level problem that prevented the job from continuing. We certainly aim to have our computers running 24/7, but crashes cannot be avoided entirely. Often, no error message will be produced in this case. In many cases, the job will be restarted automatically by a supervisor. This process may even go undetected by the end user. However, there are numerous circumstances under which the job cannot be continued for some reason. In this case, resubmitting a new job is indicated.

In any case (pipeline error with or without message, or platform error) the recommended actions are as follows:

a. wait an hour to see whether the problem fixes itself. b. resubmit the job, and see whether it fails in the same way c. modify the input (if applicable) and try again d. write to support at docking.org quoting the job id and explaining the problem only after you have tried the above.

I have privacy concerns about my data

DOCK Blaster is a free public service, run on taxpayer-supported computers. However, we do offer limited support for private calculations as follows. When you submit a job, you may provide a PIN. For the first 7 days, this PIN is necessary to access the data in the project. After 7 days, the PIN is removed, allowing public access to your job. Jobs that have not been "touched" for 14 days are removed from the system. Thus, if you want to keep your data private, we suggest deleting from our system after 6 days.

DOCK Blaster made completely wrong suggestions for my target

DOCK Blaster is a research tool aimed at helping people discover new ligands.

Is there any evidence that DOCK Blaster works?

DOCK Blaster uses the same docking technology (DOCK 3.5.54) and database technology (ZINC) as is used in the Shoichet Lab for all their publications. Furthermore, the DUD paper (JMC 2006). Furthermore, the DOCK Blaster paper (to appear).

Why are you guys doing this, I mean, DOCK Blaster?

We felt that many investigators who would like to use virtual screening were not using it because of several barriers to entry. We hope that DOCK Blaster will fill an niche and give access to this technology to investigators who previously were put off by the requirements to set up a docking laboratory.

Can I get my own private copy of DOCK Blaster?

This is something we have though about. If we get enough interest, we may be able to license DOCK Blaster technology. Please contact us to express your interest.

Does DOCK Blaster work better on some targets than on others?

Yes. Now, which ones?

How long does DOCK Blaster take?

Overall, we aim to get you preliminary results in under an hour. Big database docking typically takes a day or so, depending on many factors. Throughput depends on the load on our servers. Thank you for your patience!

What do DOCK Blaster results mean?

Top scoring hits are computer generate predictions of small molecules that might bind to your protein. Our success rate against actual drug targets is on the order of 5% or less, typically. Sometimes it is zero percent! Typically, we purchase 50 compounds that we like from the top 500 for experimental testing, and typically, we find a few that bind in the micromolar range.

Can I used DOCK Blaster with a different docking program?

Currently, DOCK Blaster only supports DOCK 3.5.54. It has not escaped our notice that the overall system may be appropriate for other docking engines. If this option interests you, please write us, making the case for a particular docking program.

Can I used DOCK Blaster with a different database of small molecules?

Yes, there are four ways to pick database subsets to dock.

• our preferred subsets
• annotated subsets
• uploaded subsets
• user-created subsets

We recommend the use of the "fragment-like" and "mini-lead-like" subsets of ZINC.

Why is it called "DOCK Blaster"?

The name is a tribute to BLAST, the famous sequence alignment and searching tool of NCBI. And of course DOCK. If you have a better name, let us know, there is a prize.

When does this (awesome) idea become reality?

DOCK Blaster has been in some sort of pre-alpha testing, in one form or another, since 2003. It entered full alpha testing involving 20+ testers on 4 continents in March 2007. If the alpha tests proceed as expected and there are no big surprises we hope to make a beta version widely available by the fall of 2007. A final public release would then appear as early as spring 2008.

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

Please use 'search' to check the documentation, use google, or try to ask our panel of experts in the blaster-fans@docking.org mailing list. If you still can't get an answer, please write support at docking.org.