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[[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.
[[DOCK Blaster]] is a free virtual screening service. These are the frequently asked questions. Questions that take more than a few lines deserve their own wiki article. Other FAQs are available at this site as follows:
* [[ZINC:FAQ]]
* [[DUD:FAQ]]
* [[DOCK:FAQ]]
* [[THC:FAQ]]
* [[FAQ]] for everything not covered by one of those products.
 
= General =


== What is DOCK Blaster? ==  
== 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.
DOCK Blaster is a free web-based service for molecular docking and virtual screening. It uses [[UCSF]] [[DOCK 3]] as a [[docking engine]], and [[ZINC]] as a [[dockable database]]. It runs entirely on the [[About our cluster | computer cluster ]] in the [[Shoichet Lab]] at [[Mission Bay]] in San Francisco. The graphical user interface comprises an expert system that is designed to help guide both novices and experts to useful results.
 
== Is DOCK Blaster formally described in a paper? How to cite? ==
 
The performance of DOCK Blaster against benchmarking data is described in Irwin, Shoichet, Mysinger et al., "Automated docking screens: a feasibility study", J. Med. Chem (2009), in press.  The documentation of the interface and the software that runs it is documented on this wiki.


== Why DOCK Blaster? Docking programs have been around for ages. What's new? ==
== 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.
We aim to serve a constituency of investigators who would like to use docking to discover new ligands for their targets, 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 biologists who seek new chemistry for their biological targets.


== How do I use DOCK Blaster? ==
== 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 [http://blaster.docking.org/] to get started.
 
Please see [[DOCK Blaster | What you need to start]].


== How much does DOCK Blaster cost to use? ==
== 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.
DOCK Blaster is free. It is supported by the US National Institutes of Health via grant GM71896 (to JJI and BKS). We reserve the right to limit usage by intensive users.


== I'm having trouble using DOCK Blaster ==
== What do I do if I am 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.
Please see the [[DOCK Blaster:Problems]] page for DOCK Blaster specific problems.


== Can I trust DOCK Blaster? ==
If you began by uploaded a receptor file, aka "Start with a structure", by far the most common problem is with the formatting of the files. We recommend reading [[DOCK_Blaster:Prepare_Input | this]] and also looking at some [[DOCK_Blaster:Tutorials | examples]] and also [http://data.docking.org sample data].
This question warrants its own article. [[DOCK Blaster:Reliability]]


== I think DOCK Blaster has crashed on my job ==
If you began with a PDB code, aka "Start with a PDB Code", by far the most common problem is that there is no single identifiable ligand in the file. If this is the case, you need to download the PDB file yourself, and, specifying the binding site, use the "Start with a structure" starting point.  
"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.
If you used "I'm feeling lucky", and you are having problems, we regret that you were not more lucky. We suggest trying "I'm feeling lucky" a couple of more times, and perhaps your luck will change.  


In any case (pipeline error with or without message, or platform error) the recommended actions are as follows:
More detailed information about problems may be found here:


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.


* [[Problems]] page for a general overview of all problems.


== I have privacy concerns about my data ==
* [[Bugs]] page for information about bugs. Please report bugs to support at docking.org.  
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 is reporting a problem that I don't think is real/legitimate ==
* [[DOCK Blaster:Problems]] page for DOCK Blaster specific problems.


== DOCK Blaster made completely wrong suggestions for my target ==
== Can DOCK Blaster be trusted? ==
DOCK Blaster is a research tool aimed at helping people discover new ligands.
Please see [[DOCK Blaster:Reliability | this]].
 
== Has DOCK Blaster crashed? ==
Please read [[DOCK Blaster:Crash  | this]].
 
== Are my data private? ==
Please see our [[Privacy Policy]]
 
== What should I do if I disagree with a decision DOCK Blaster has apparently made? ==
Please write to support at docking.org explaining the problem.
 
== What should I do if DOCK Blaster has made completely wrong suggestions for my target? ==
DOCK Blaster is a research tool that aims to help people discover new ligands.  Unfortunately, docking can fail for many reasons, as documented by an extensive literature. Our benchmarking studies (Irwin et al, J Med Chem, 2009) suggest that black box docking works on perhaps 18% of eligible targets.  Thus there is a rather high probability that your target is not among the successful ones.  Finally, it is important to remain skeptical of any docking results, whether they are produced by an expert or a machine like DOCK Blaster.


== Is there any evidence that DOCK Blaster works? ==
== 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).
DOCK Blaster uses the same docking technology (DOCK 3) and database technology (ZINC) as is used in the Shoichet Lab for all their ([http://shoichetlab.compbio.ucsf.edu/publications.php publications]). The DUD Paper (Huang, Shoichet Irwin, J Med Chem, 2006) assessed the performance of docking, some of it fully automated. Recently, the DOCK Blaster paper (Irwin et al, J Med Chem 2009, in press) assessed fully automated docking against over 7000 targets drawn from the PDB.  The results indicate that automated docking screens produce viable-looking results perhaps 18% of the time.  Importantly, the automatic self-assessment feature of DOCK Blaster allows you to tell when this is true.


== Why are you guys doing this, I mean, DOCK Blaster? ==
== What is your motivation to create and support 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.
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? ==
== 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.
You may request a copy of DOCK Blaster by writing to John Irwin at jji at cgl dot ucsf dot edu. We will be making the scripts available, but it will take us some time following publication (Sept 2009) to get them into a state we can release.


== Does DOCK Blaster work better on some targets than on others? ==
== Does DOCK Blaster work better on some targets than on others? ==
Yes. Now, which ones?  
Yes. Now, which ones? The paper (Irwin et al, J Med Chem, 2009, in press) documents 1,298 targets for which DOCK Blaster produces viable-looking results. You can find these on our [http://data.docking.org website].  [http://data.docking.org/2009/TableS12.xls TableS12.xls]


== How long does DOCK Blaster take? ==
== 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!
Submitted to an unloaded cluster, preliminary docking usually runs in 30-60 minutes. A full database screen, which may or may not be warranted by the preliminary docking, can take hours to days, depending on the binding site and the database docked. If the cluster is loaded it will obviously take longer to deliver results.  We aim to provide informative messages to manage your expectations. Thank you for your patience! More information here: [[DOCK Blaster:Timings]]


== What do DOCK Blaster results mean? ==
== 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.
Top scoring hits from a docking screen are computer-generated predictions of small molecules that may bind to your protein. Surveying the literature, typical prediction rates from docking screens vary wildly, but are often of a rate of only a few percent, although there are famous exceptions (Doman 2002). In a typical screen, purchasing 50 compounds selected from among the top 500, we would consider ourselves fortunate if 3 compounds showed micromolar affinity.  What this means in practice is that docking hit lists should not be simply purchased willy-nilly.  We recommend holding a [[hit picking party]] to select compounds for purchase and test based on a range of opinions.  We would be astonished to see a confirmed hit rate over 10%, meaning that we expect at least 9/10 top scoring docking compounds WILL NOT BIND.  Caveat emptor.


== Can I used DOCK Blaster with a different docking program? ==
== 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.
Currently, DOCK Blaster only supports DOCK 3. 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? ==
== Can I used DOCK Blaster with my own database of small molecules? ==
Yes, there are four ways to pick database subsets to dock.  
Yes, to some extent.  You can upload ligands to ZINC to create an user uploaded subset, 1000 molecules at a time. These subsets may be docked using DOCK Blaster.
* 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.
A number of subsets of ZINC are available for docking.  We may be able to create large custom subsets to suit your purposes.  If you do not see what you need in the "by subset" page of ZINC, please write us at support at docking.org to discuss.


For most purposes, we recommend the use of the "fragment-like" or "lead-like" subsets of ZINC.


== Why is it called "DOCK Blaster"? ==
== 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.  
The name is a tribute to [http://www.ncbi.nlm.nih.gov/BLAST/ BLAST], the famous sequence alignment and searching tool of [http://www.ncbi.nlm.nih.gov/ NCBI]. And of course [[Portal:DOCK | DOCK]]. If you have a better name, let us know, there is a prize. ;-)
 
== What is the history of DOCK Blaster? ==
Please see [[DOCK Blaster:History]].
 
= Preparer / Scrutinizer Questions =


== 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.


= Calibration Questions =


== I have a question that isn't listed here... ==
 
= Docking Questions =
 
 
= Results Browser and Interpretation Questions =
 
 
 
= What do I do if my question is not 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.
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.
[[Category:DOCK Blaster]]
[[Category:FAQ]]

Latest revision as of 22:06, 5 April 2013

DOCK Blaster is a free virtual screening service. These are the frequently asked questions. Questions that take more than a few lines deserve their own wiki article. Other FAQs are available at this site as follows:

General

What is DOCK Blaster?

DOCK Blaster is a free web-based service for molecular docking and virtual screening. It uses UCSF DOCK 3 as a docking engine, and ZINC as a dockable database. It runs entirely on the computer cluster in the Shoichet Lab at Mission Bay in San Francisco. The graphical user interface comprises an expert system that is designed to help guide both novices and experts to useful results.

Is DOCK Blaster formally described in a paper? How to cite?

The performance of DOCK Blaster against benchmarking data is described in Irwin, Shoichet, Mysinger et al., "Automated docking screens: a feasibility study", J. Med. Chem (2009), in press. The documentation of the interface and the software that runs it is documented on this wiki.

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

We aim to serve a constituency of investigators who would like to use docking to discover new ligands for their targets, 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 biologists who seek new chemistry for their biological targets.

How do I use DOCK Blaster?

Please see What you need to start.

How much does DOCK Blaster cost to use?

DOCK Blaster is free. It is supported by the US National Institutes of Health via grant GM71896 (to JJI and BKS). We reserve the right to limit usage by intensive users.

What do I do if I am having trouble using DOCK Blaster?

If you began by uploaded a receptor file, aka "Start with a structure", by far the most common problem is with the formatting of the files. We recommend reading this and also looking at some examples and also sample data.

If you began with a PDB code, aka "Start with a PDB Code", by far the most common problem is that there is no single identifiable ligand in the file. If this is the case, you need to download the PDB file yourself, and, specifying the binding site, use the "Start with a structure" starting point.

If you used "I'm feeling lucky", and you are having problems, we regret that you were not more lucky. We suggest trying "I'm feeling lucky" a couple of more times, and perhaps your luck will change.

More detailed information about problems may be found here:


  • Problems page for a general overview of all problems.
  • Bugs page for information about bugs. Please report bugs to support at docking.org.

Can DOCK Blaster be trusted?

Please see this.

Has DOCK Blaster crashed?

Please read this.

Are my data private?

Please see our Privacy Policy

What should I do if I disagree with a decision DOCK Blaster has apparently made?

Please write to support at docking.org explaining the problem.

What should I do if DOCK Blaster has made completely wrong suggestions for my target?

DOCK Blaster is a research tool that aims to help people discover new ligands. Unfortunately, docking can fail for many reasons, as documented by an extensive literature. Our benchmarking studies (Irwin et al, J Med Chem, 2009) suggest that black box docking works on perhaps 18% of eligible targets. Thus there is a rather high probability that your target is not among the successful ones. Finally, it is important to remain skeptical of any docking results, whether they are produced by an expert or a machine like DOCK Blaster.

Is there any evidence that DOCK Blaster works?

DOCK Blaster uses the same docking technology (DOCK 3) and database technology (ZINC) as is used in the Shoichet Lab for all their (publications). The DUD Paper (Huang, Shoichet Irwin, J Med Chem, 2006) assessed the performance of docking, some of it fully automated. Recently, the DOCK Blaster paper (Irwin et al, J Med Chem 2009, in press) assessed fully automated docking against over 7000 targets drawn from the PDB. The results indicate that automated docking screens produce viable-looking results perhaps 18% of the time. Importantly, the automatic self-assessment feature of DOCK Blaster allows you to tell when this is true.

What is your motivation to create and support 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?

You may request a copy of DOCK Blaster by writing to John Irwin at jji at cgl dot ucsf dot edu. We will be making the scripts available, but it will take us some time following publication (Sept 2009) to get them into a state we can release.

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

Yes. Now, which ones? The paper (Irwin et al, J Med Chem, 2009, in press) documents 1,298 targets for which DOCK Blaster produces viable-looking results. You can find these on our website. TableS12.xls

How long does DOCK Blaster take?

Submitted to an unloaded cluster, preliminary docking usually runs in 30-60 minutes. A full database screen, which may or may not be warranted by the preliminary docking, can take hours to days, depending on the binding site and the database docked. If the cluster is loaded it will obviously take longer to deliver results. We aim to provide informative messages to manage your expectations. Thank you for your patience! More information here: DOCK Blaster:Timings

What do DOCK Blaster results mean?

Top scoring hits from a docking screen are computer-generated predictions of small molecules that may bind to your protein. Surveying the literature, typical prediction rates from docking screens vary wildly, but are often of a rate of only a few percent, although there are famous exceptions (Doman 2002). In a typical screen, purchasing 50 compounds selected from among the top 500, we would consider ourselves fortunate if 3 compounds showed micromolar affinity. What this means in practice is that docking hit lists should not be simply purchased willy-nilly. We recommend holding a hit picking party to select compounds for purchase and test based on a range of opinions. We would be astonished to see a confirmed hit rate over 10%, meaning that we expect at least 9/10 top scoring docking compounds WILL NOT BIND. Caveat emptor.

Can I used DOCK Blaster with a different docking program?

Currently, DOCK Blaster only supports DOCK 3. 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 my own database of small molecules?

Yes, to some extent. You can upload ligands to ZINC to create an user uploaded subset, 1000 molecules at a time. These subsets may be docked using DOCK Blaster.

A number of subsets of ZINC are available for docking. We may be able to create large custom subsets to suit your purposes. If you do not see what you need in the "by subset" page of ZINC, please write us at support at docking.org to discuss.

For most purposes, we recommend the use of the "fragment-like" or "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. ;-)

What is the history of DOCK Blaster?

Please see DOCK Blaster:History.

Preparer / Scrutinizer Questions

Calibration Questions

Docking Questions

Results Browser and Interpretation Questions

What do I do if my question is not 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.