DOCK Blaster:Philosophy - Revision history

Therese: 14 revisions

2012-10-08T20:02:09Z

14 revisions

← Older revision

Revision as of 20:02, 8 October 2012

2009-08-10T20:04:58Z

Tools for Self Evaluation

← Older revision		Revision as of 20:04, 10 August 2009
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	== 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 ==

2009-08-10T20:04:06Z

Expert System to Interpret Input

← Older revision		Revision as of 20:04, 10 August 2009
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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:
	* 0. no problems. files were used as supplied		* no problems. files were used as supplied
	* 1. minor changes. job submitted. full details of changes made. updated files available.		* minor changes. job submitted. full details of changes made. updated files available.
	* 2. major changes were necessary. Here are the files we changed. You must confirm to proceed.		* major changes were necessary. Here are the files we changed. You must confirm to proceed.
	* 3. unresolvable problems. the job cannot start without manual changes by you to the input files.		* unresolvable problems. the job cannot start without manual changes by you to the input files.

	== Tools for Self Evaluation ==		== Tools for Self Evaluation ==

2009-08-10T20:03:39Z

Fair Share

← Older revision		Revision as of 20:03, 10 August 2009
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	== Fair Share ==		== Fair Share ==
	We meter use based on IP address ~~based on~~ time ~~periods~~: ~~minutes, hours, days, and weeks~~. ~~Two mechanisms allow increased usage: privileges and vouchers~~. ~~Privileges are assigned based on IP address, and offer a higher number of transactions per time period~~. ~~Vouchers are a IP-free means of performing more transactions~~. We also allow authentication to acquire more rights. We expect ~~most~~ users ~~will not require special privileges~~.		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 ==

2009-08-10T20:00:18Z

Registration

← Older revision		Revision as of 20:00, 10 August 2009
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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 ==

2009-08-10T19:59:20Z

Motivation

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	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.		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 ~~the useful technology of virtual screening~~ more accessible to investigators who can benefit from it. We are particularly interested in helping non-specialists who otherwise could not afford to set up a computing lab.		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.

	{{TOCright}}		{{TOCright}}

2009-02-26T14:59:30Z

← Older revision		Revision as of 14:59, 26 February 2009
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	== Privacy ==		== Privacy ==
	We cannot and do not guarantee privacy of your data.		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.



	[[Category:DOCK Blaster]]		[[Category:DOCK Blaster]]
	[[Category:Opinion]]		[[Category:Opinion]]

2009-02-26T14:53:47Z

Tools for Self Evaluation

← Older revision		Revision as of 14:53, 26 February 2009
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	== Tools for Self Evaluation ==		== Tools for Self Evaluation ==
	A common concern with docking calculations is whether the results are ~~meaningful~~. 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.		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.


	== Privacy ==		== Privacy ==

2009-02-26T14:52:12Z

Privacy

← Older revision		Revision as of 14:52, 26 February 2009
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	== Privacy ==		== Privacy ==
	We cannot guarantee privacy of your data.		We cannot and do not guarantee privacy of your data.


	[[Category:DOCK Blaster]]		[[Category:DOCK Blaster]]
	[[Category:Opinion]]		[[Category:Opinion]]

2009-02-26T14:51:49Z

Expert System to Interpret Input

← Older revision		Revision as of 14:51, 26 February 2009
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	* 0. no problems. files were used as supplied		* 0. no problems. files were used as supplied
	* 1. minor changes. job submitted. full details of changes made. updated files available.		* 1. minor changes. job submitted. full details of changes made. updated files available.
	* 2. major ~~chnages~~.		* 2. major changes were necessary. Here are the files we changed. You must confirm to proceed.
	* 3. unresolvable problems.		* 3. unresolvable problems. the job cannot start without manual changes by you to the input files.


	== Tools for Self Evaluation ==		== Tools for Self Evaluation ==