Difference between revisions of "DOCK Blaster:FAQ"

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== Q1. What is DOCK Blaster? ==  
 
== Q1. What is DOCK Blaster? ==  
 +
DOCK Blaster is a free 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 San Francisco. The interface is an expert system that tries to help you get results you can use. We hope to publish a paper in 2007.
  
 
== Q2. How do I use DOCK Blaster? ==
 
== Q2. How do I use DOCK Blaster? ==
 +
You need a structure of your target, and an indication of the binding site you want to target. The target should be in PDB format, and must conform to certain rules (see [[Preparing Input]]. The binding site indicator 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? ==
 
== Q3. How much does DOCK Blaster cost to use? ==
 +
DOCK Blaster is completely free. It is supported by NIH grant GM 71896 (to BKS and JJI).
  
 
== Q4. I'm having trouble using DOCK Blaster ==
 
== Q4. I'm having trouble using DOCK Blaster ==
 +
There are broadly speaking three kinds of problems
 +
1. The site is broken or seems to be acting 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. We have tried to make the error messages as descriptive as possible. 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. The job has run, but you cannot understand what to do with the results.
  
 
== Q5. Can I trust DOCK Blaster? ==
 
== 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 ==
 
== 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 ==
 
== 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 
  
 
== Q8. DOCK Blaster is reporting a problem that I don't think is real/legitimate ==
 
== Q8. DOCK Blaster is reporting a problem that I don't think is real/legitimate ==

Revision as of 06:12, 14 February 2007

DOCK Blaster FAQ

Q1. What is DOCK Blaster?

DOCK Blaster is a free 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 San Francisco. The interface is an expert system that tries to help you get results you can use. We hope 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 you want to target. The target should be in PDB format, and must conform to certain rules (see Preparing Input. The binding site indicator 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 completely free. It is supported by NIH grant GM 71896 (to BKS and JJI).

Q4. I'm having trouble using DOCK Blaster

There are broadly speaking three kinds of problems

1. The site is broken or seems to be acting 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. We have tried to make the error messages as descriptive as possible. 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. The job has run, but you cannot understand what to do with the results. 

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

Q8. DOCK Blaster is reporting a problem that I don't think is real/legitimate

Q9. DOCK Blaster made completely wrong suggestions for my target

Q10. Is there any evidence that DOCK Blaster works?

Q11. Why are you guys doing this, I mean, DOCK Blaster?

Q12. Can I get my own private copy of DOCK Blaster?

Q13. Does DOCK Blaster work better on some targets than on others?

Q14. How long does DOCK Blaster take?

Q15. What do DOCK Blaster results mean?

Q16. Can I used DOCK Blaster with a different docking program?

Q17. Can I used DOCK Blaster with a different database of small molecules?

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