DOCK Blaster:Preliminaries - Revision history

Therese: 35 revisions

2012-10-08T20:02:10Z

35 revisions

← Older revision	Revision as of 20:02, 8 October 2012
(No difference)

Frodo at 19:22, 11 May 2011

2011-05-11T19:22:24Z

← Older revision		Revision as of 19:22, 11 May 2011
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	Docking requires three things: a target structure, a database, and a docking program. [[DOCK Blaster]] uses [[DOCK 3~~.5.54~~]] as the docking program and various [[ZINC Database]] subsets as the database. It is up to you to choose a target structure for docking. You will also need to have some idea of the binding site you wish to target, as proteins often contain more than one eligible site. You may also have additional information such as actives and inactives, which can be helpful for assessing docking performance and viability.		Docking requires three things: a target structure, a database, and a docking program. [[DOCK Blaster]] uses [[DOCK 3]] as the docking program and various [[ZINC Database]] subsets as the database. It is up to you to choose a target structure for docking. You will also need to have some idea of the binding site you wish to target, as proteins often contain more than one eligible site. You may also have additional information such as actives and inactives, which can be helpful for assessing docking performance and viability.

	{{TOCright}}		{{TOCright}}

Frodo: /* No good crystal structure available */

2009-09-09T03:08:02Z

No good crystal structure available

← Older revision		Revision as of 03:08, 9 September 2009
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	== No good crystal structure available ==		== No good crystal structure available ==
	A good crystal structure is generally one that has 2.5 A resolution or better, and no serious problems (e.g. as reported by PROCHECK). In the absence of a good crystal structure, you may still be able to start docking using another kind of target structure.		A good crystal structure is generally one that has 2.5 A resolution or better, and no serious problems (e.g. as reported by PROCHECK). Missing density in the binding site is a big problem. Disorder can often be resolved, at least mechanically, by simply picking one of the disorder models. We often pick "A". In the absence of a good crystal structure, you may still be able to start docking using another kind of target structure.

	=== Comparative model ===		=== Comparative model ===

Frodo: /* What is the question? */

2009-07-14T23:28:09Z

What is the question?

← Older revision		Revision as of 23:28, 14 July 2009
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	* 2) Are the docking results worth spending time and money testing?		* 2) Are the docking results worth spending time and money testing?

	Ideally, we would like to answer question 2 first. DOCK Blaster's approach is to request that you collect available control information, in the form of bound ligands, actives and inactives that may be reported in the literature, databases or patents, or known from other sources. DOCK Blaster performs a preliminary docking study which attempts to recapitulate known experimental information. If it cannot do this, it does not necessairily mean that docking "does not work". There may be good mitigating circumstances. However, it should raise doubt in your mind if docking cannot ~~re-discover~~ what you already know.		Ideally, we would like to answer question 2 first. DOCK Blaster's approach is to request that you collect available control information, in the form of bound ligands, actives and inactives that may be reported in the literature, databases or patents, or known from other sources. DOCK Blaster performs a preliminary docking study which attempts to recapitulate known experimental information. If it cannot do this, it does not necessairily mean that docking "does not work". There may be good mitigating circumstances. However, it should raise doubt in your mind if docking cannot recapitulate what you already know.

	Here we consider some of the most typical scenarios for a docking project, and attempt to point out what you should keep in mind before you start docking. Remember, this is research! So be sure to do controls whenever you can, and remain skeptical!		Here we consider some of the most typical scenarios for a docking project, and attempt to point out what you should keep in mind before you start docking. Remember, this is research! So be sure to do controls whenever you can, and remain skeptical!

Frodo: /* What is the question? */

2009-07-14T23:27:15Z

What is the question?

← Older revision		Revision as of 23:27, 14 July 2009
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	* 2) Are the docking results worth spending time and money testing?		* 2) Are the docking results worth spending time and money testing?

	Ideally, we would like to answer question 2 first. DOCK Blaster's approach is to collect available control information, in the form of bound ligands, actives and inactives that may be reported in the literature, databases or patents, or known from other sources. DOCK Blaster performs a preliminary docking study which attempts to recapitulate known experimental information. If it cannot do this, it does not necessairily mean that docking "does not work". There may be good mitigating circumstances. However, it should raise doubt in your mind if docking cannot re-discover what you already know.		Ideally, we would like to answer question 2 first. DOCK Blaster's approach is to request that you collect available control information, in the form of bound ligands, actives and inactives that may be reported in the literature, databases or patents, or known from other sources. DOCK Blaster performs a preliminary docking study which attempts to recapitulate known experimental information. If it cannot do this, it does not necessairily mean that docking "does not work". There may be good mitigating circumstances. However, it should raise doubt in your mind if docking cannot re-discover what you already know.

	Here we consider some of the most typical scenarios for a docking project, and attempt to point out what you should keep in mind before you start docking. Remember, this is research! So be sure to do controls whenever you can, and remain skeptical!		Here we consider some of the most typical scenarios for a docking project, and attempt to point out what you should keep in mind before you start docking. Remember, this is research! So be sure to do controls whenever you can, and remain skeptical!

Frodo at 00:59, 13 February 2009

2009-02-13T00:59:58Z

← Older revision		Revision as of 00:59, 13 February 2009
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	Docking requires three things: a target structure, a database, and a docking program. [[DOCK Blaster]] uses [[DOCK 3.5.54]] as the docking program and various [[ZINC]] subsets as the database. It is up to you to choose a target structure for docking. You will also need to have some idea of the binding site you wish to target, as proteins often contain more than one eligible site. You may also have additional information such as actives and inactives, which can be helpful for assessing docking performance and viability.		Docking requires three things: a target structure, a database, and a docking program. [[DOCK Blaster]] uses [[DOCK 3.5.54]] as the docking program and various [[ZINC Database]] subsets as the database. It is up to you to choose a target structure for docking. You will also need to have some idea of the binding site you wish to target, as proteins often contain more than one eligible site. You may also have additional information such as actives and inactives, which can be helpful for assessing docking performance and viability.

	{{TOCright}}		{{TOCright}}

Frodo: /* Is docking going to work for me? */

2009-02-12T19:50:48Z

Is docking going to work for me?

← Older revision		Revision as of 19:50, 12 February 2009
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	DOCK Blaster performs control calculations using supplied actives and inactives, and in particular a docked crystallographic ligand. If docking is able to recapitulate experimentally known information, this should be very reassuring. If docking does not recapitulate experimentally known information, whether the pose of a crystallographically ligand or its rank among the top of property-matched decoys, it is not a show stopper. But failure to reproduce known information during preliminary calculations should be viewed as a serious challenge to the viability of the docking model. If possible, experiment with the structure, to see whether better results can be obtained prior to starting a database screen.		DOCK Blaster performs control calculations using supplied actives and inactives, and in particular a docked crystallographic ligand. If docking is able to recapitulate experimentally known information, this should be very reassuring. If docking does not recapitulate experimentally known information, whether the pose of a crystallographically ligand or its rank among the top of property-matched decoys, it is not a show stopper. But failure to reproduce known information during preliminary calculations should be viewed as a serious challenge to the viability of the docking model. If possible, experiment with the structure, to see whether better results can be obtained prior to starting a database screen.




	[[Category:DOCK Blaster]]		[[Category:DOCK Blaster]]
	[[Category:User guide]]		[[Category:User guide]]

Frodo: /* Is docking going to work for me? */

2009-02-12T19:50:15Z

Is docking going to work for me?

← Older revision		Revision as of 19:50, 12 February 2009
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	= Is docking going to work for me? =		= Is docking going to work for me? =

			DOCK Blaster performs control calculations using supplied actives and inactives, and in particular a docked crystallographic ligand. If docking is able to recapitulate experimentally known information, this should be very reassuring. If docking does not recapitulate experimentally known information, whether the pose of a crystallographically ligand or its rank among the top of property-matched decoys, it is not a show stopper. But failure to reproduce known information during preliminary calculations should be viewed as a serious challenge to the viability of the docking model. If possible, experiment with the structure, to see whether better results can be obtained prior to starting a database screen.

	[[Category:DOCK Blaster]]		[[Category:DOCK Blaster]]
	[[Category:User guide]]		[[Category:User guide]]

Frodo: /* What should I worry about? */

2009-02-12T19:47:08Z

What should I worry about?

← Older revision		Revision as of 19:47, 12 February 2009
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	* pH at which the structure was solved / is biologically relevant		* pH at which the structure was solved / is biologically relevant

	= What should I worry about? =		= What should I worry about? =

			* water structure
			* HIS protonation
			*

	= Is docking going to work for me? =		= Is docking going to work for me? =

Frodo: /* Additional information = */

2009-02-12T19:46:28Z

Additional information =

← Older revision		Revision as of 19:46, 12 February 2009
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	* You may be able to use atoms from multiple bound ligands as "hot spots".		* You may be able to use atoms from multiple bound ligands as "hot spots".

	== Additional information ===		== Additional information ==

	=== Actives and Inactives ===		=== Actives and Inactives ===