DOCK Blaster:Philosophy: Difference between revisions
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== Registration == | == Registration == | ||
We deliberately do not require registration to use DOCK Blaster. We have done this to keep the barriers to its use low. | We deliberately do not require registration to use DOCK Blaster. We have done this to keep the barriers to its use low. Usage is anonymous and we do not look at your data unless you ask us to (and even then we may not have time). | ||
== Fair Share == | == Fair Share == | ||
We meter use based on IP address | We meter use based on IP address by time using a | ||
[http://blaster.docking.org/cgi-bin/myquotas.pl quota system]. We also allow authentication to acquire more rights. We expect basic quotas will be sufficient for nearly all users. | |||
== Novice vs Expert == | == Novice vs Expert == | ||
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== Expert System to Interpret Input == | == Expert System to Interpret Input == | ||
The DOCK Blaster expert system attempts to make sensible choices based on the input you supply, and to resolve most minor issues in a reasonable fashion. There are four outcomes from uploading files: | The DOCK Blaster expert system attempts to make sensible choices based on the input you supply, and to resolve most minor issues in a reasonable fashion. There are four outcomes from uploading files: | ||
* | * no problems. files were used as supplied | ||
* | * minor changes. job submitted. full details of changes made. updated files available. | ||
* | * major changes were necessary. Here are the files we changed. You must confirm to proceed. | ||
* | * unresolvable problems. the job cannot start without manual changes by you to the input files. | ||
== Tools for Self Evaluation == | == Tools for Self Evaluation == | ||
A common concern with docking calculations is whether the results are worth investing money and time to test. We recognize this problem, and realise that a perfect solution is probably unattainable. Our pragmatic approach is to provide you with calibration data so you can evaluate for yourself how well the docking is working. This is why a docked ligand as a control is so important for evaluating a docking model. | A common concern with docking calculations is whether the results are worth investing money and time to test. We recognize this problem, and realise that a perfect solution is probably unattainable. Our pragmatic approach is to provide you with calibration data so you can evaluate for yourself how well the docking is working. This is why a docked ligand as a control is so important for evaluating a docking model. This is discussed extensively in our J Med Chem paper: Irwin, Shoichet, Mysinger et al, J Med Chem (2009), in press. | ||
== Privacy == | == Privacy == | ||
Latest revision as of 20:02, 8 October 2012
Motivation
There are many free (to academics) docking programs. Having a docking program installed on your local computer gives you much more control that we can possibly offer with DOCK Blaster. What is the motivation for DOCK Blaster?
Installing and running a docking program is a significant barrier to entry for many investigators. We ourselves find we would like to run other docking programs, but balk at the cost in time to acquire, install, and become comfortable with each program.
There is a pressing need to make docking screens more accessible to investigators such as biologists and medicinal chemists who can benefit from it. We are particularly interested in helping non-specialists who otherwise could not afford to set up a computing lab.
Registration
We deliberately do not require registration to use DOCK Blaster. We have done this to keep the barriers to its use low. Usage is anonymous and we do not look at your data unless you ask us to (and even then we may not have time).
We meter use based on IP address by time using a quota system. We also allow authentication to acquire more rights. We expect basic quotas will be sufficient for nearly all users.
Novice vs Expert
DOCK Blaster is designed to be as simple and clear as possible. There are several mechanisms that can give an expert greater control than that afforded by the basic graphical user interface. The expert.tar input field. The XML RPC interface. We expect most users will not need expert access. For more info, write to us.
Expert System to Interpret Input
The DOCK Blaster expert system attempts to make sensible choices based on the input you supply, and to resolve most minor issues in a reasonable fashion. There are four outcomes from uploading files:
- no problems. files were used as supplied
- minor changes. job submitted. full details of changes made. updated files available.
- major changes were necessary. Here are the files we changed. You must confirm to proceed.
- unresolvable problems. the job cannot start without manual changes by you to the input files.
Tools for Self Evaluation
A common concern with docking calculations is whether the results are worth investing money and time to test. We recognize this problem, and realise that a perfect solution is probably unattainable. Our pragmatic approach is to provide you with calibration data so you can evaluate for yourself how well the docking is working. This is why a docked ligand as a control is so important for evaluating a docking model. This is discussed extensively in our J Med Chem paper: Irwin, Shoichet, Mysinger et al, J Med Chem (2009), in press.
Privacy
We cannot and do not guarantee privacy of your data.
Cost
DOCK Blaster, ZINC, DUD, HEI, SEA and other docking.org tools are funded by the US taxpayer via NIH GM71896, and are free to use for everyone. We intend to keep them free to use as long as we are funded.