Choosing a subset - Revision history

Frodo at 03:07, 14 February 2014

2014-02-14T03:07:46Z

← Older revision		Revision as of 03:07, 14 February 2014
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	-- John Irwin		-- John Irwin

			[[Category:Docking]]
			[[Category:Theory]]

Therese: 5 revisions

2012-10-08T18:10:31Z

5 revisions

← Older revision	Revision as of 18:10, 8 October 2012
(No difference)

Frodo: /* Property-filtered subsets */

2009-09-01T05:52:40Z

Property-filtered subsets

← Older revision		Revision as of 05:52, 1 September 2009
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	We particularly favor subset #2 (fragment like) and #1 (lead like) for many reasons: solubility, sampling of chemical space / Hann complexity, fewer docking artifacts.		We particularly favor subset #2 (fragment like) and #1 (lead like) for many reasons: solubility, sampling of chemical space / Hann complexity, fewer docking artifacts.

	We offer "normal" ~~submits~~ (1-10), "clean" subsets, with compounds that are thought to cause artifacts under some conditions (11-20) and "now" subsets, which included only compounds that can probably be sourced within 2 weeks.		We offer "normal" subsets (1-10), "clean" subsets, with compounds that are thought to cause artifacts under some conditions (11-20) and "now" subsets, which included only compounds that can probably be sourced within 2 weeks.

	For DOCK Blaster, we currently only allow docking subsets under 1 million compounds. We are working on a free lead like subset. Currently, lead like is a little too big.		For DOCK Blaster, we currently only allow docking subsets under 1 million compounds. We are working on a free lead like subset. Currently, lead like is a little too big.

	== User created subsets ==		== User created subsets ==

Frodo at 17:41, 31 August 2009

2009-08-31T17:41:40Z

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			{{TOCright}}

	What subset of ZINC should I dock? Here is a quick guide.		What subset of ZINC should I dock? Here is a quick guide.

	~~First, what~~ subsets are available?		= What subsets are available? =

	1. Vendor Subsets (for immediate delivery)		== Vendor Subsets (for immediate delivery) ==
	Use these if you have a deal with a vendor that makes pricing attractive. For instance, even if you don't pre-order a screening library, many vendors will offer special pricing for volume orders.		Use these if you have a deal with a vendor that makes pricing attractive. For instance, even if you don't pre-order a screening library, many vendors will offer special pricing for volume orders.

	2. Virtual Vendor subsets (typically 8-10 weeks delivery).		== Virtual Vendor subsets (typically 8-10 weeks delivery) ==
	Use these if rapid turnaround is not essential. Advantages: gives you access to over twice as many compounds as the "immediate delivery" subsets.		Use these if rapid turnaround is not essential. Advantages: gives you access to over twice as many compounds as the "immediate delivery" subsets.

	3. Property-filtered subsets.		== Property-filtered subsets ==
	We particularly favor subset #2 (fragment like) and #1 (lead like) for many reasons: solubility, sampling of chemical space / Hann complexity, fewer docking artifacts.		We particularly favor subset #2 (fragment like) and #1 (lead like) for many reasons: solubility, sampling of chemical space / Hann complexity, fewer docking artifacts.

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	For DOCK Blaster, we currently only allow docking subsets under 1 million compounds. We are working on a free lead like subset. Currently, lead like is a little too big.		For DOCK Blaster, we currently only allow docking subsets under 1 million compounds. We are working on a free lead like subset. Currently, lead like is a little too big.

	4. User created subsets.		== User created subsets ==
	These are subsets created by users, from the search results page, using the "create subsets" button. Some are also created as byproducts of DOCK Blaster runs.		These are subsets created by users, from the search results page, using the "create subsets" button. Some are also created as byproducts of DOCK Blaster runs.

	5. User-uploaded subsets.		== User-uploaded subsets ==
	These are compounds uploaded by users. If you uploaded molecules you want to dock, this is where to go.		These are compounds uploaded by users. If you uploaded molecules you want to dock, this is where to go.

	6. By annotation.		== By annotation ==
	You may want to dock compounds that have been pre-filtered for their likelihood of binding to certain targets, based on literature reports and patents. This option is not currently supported.		You may want to dock compounds that have been pre-filtered for their likelihood of binding to certain targets, based on literature reports and patents. This option is not currently supported.

	7. By 2D prediction.		== By 2D prediction ==
	You may want to dock compounds that resemble actives, based on their similarity to ensembles of actives (SEA). This option is not currently supported.		You may want to dock compounds that resemble actives, based on their similarity to ensembles of actives (SEA). This option is not currently supported.

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	= What should I dock? =		= What should I dock? =
	Relatively small binding site: start with "clean-fragments" (by property, #12). Larger binding site, start with "clean-leads" (by property #11). There are of course exceptions to these rules, but these are sensible starting points.		Relatively small binding site: start with "clean-fragments" (by property, #12). Larger binding site, start with "clean-leads" (by property #11). There are of course exceptions to these rules, but these are sensible starting points.

			= Notes for DOCK Blaster users =
			1. We only let you dock smaller subsets online for free. Currently 1.3 million is the cutoff. Write us if this is a problem for you.

			2. You need to refer to the ZINC "by vendor" and "by subset" pages to get more information about the subsets. We have deliberately kept the pull down menu on the DOCK Blaster "Calibration done" page simple. Just open ZINC in another browser window to understand the abbreviations.



	-- John Irwin		-- John Irwin

Frodo at 17:23, 31 August 2009

2009-08-31T17:23:53Z

← Older revision		Revision as of 17:23, 31 August 2009
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	3. Property-filtered subsets.		3. Property-filtered subsets.
	We particularly favor subset #2 (fragment like) and #1 (lead like) for many reasons: solubility, sampling of chemical space / Hann complexity, fewer docking artifacts.		We particularly favor subset #2 (fragment like) and #1 (lead like) for many reasons: solubility, sampling of chemical space / Hann complexity, fewer docking artifacts.

			We offer "normal" submits (1-10), "clean" subsets, with compounds that are thought to cause artifacts under some conditions (11-20) and "now" subsets, which included only compounds that can probably be sourced within 2 weeks.

			For DOCK Blaster, we currently only allow docking subsets under 1 million compounds. We are working on a free lead like subset. Currently, lead like is a little too big.

	4. User created subsets.		4. User created subsets.

Frodo: /* What should I dock? */

2009-05-14T16:14:12Z

What should I dock?

← Older revision		Revision as of 16:14, 14 May 2009
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	= What should I dock? =		= What should I dock? =
	Relatively small binding site: start with "~~fragment like~~" (by property, #2). Larger binding site, start with "~~lead like~~" (by property #1).		Relatively small binding site: start with "clean-fragments" (by property, #12). Larger binding site, start with "clean-leads" (by property #11). There are of course exceptions to these rules, but these are sensible starting points.


	-- John Irwin		-- John Irwin

Frodo at 18:44, 22 July 2008

2008-07-22T18:44:20Z

New page

What subset of ZINC should I dock? Here is a quick guide.

First, what subsets are available?

1. Vendor Subsets (for immediate delivery)
Use these if you have a deal with a vendor that makes pricing attractive. For instance, even if you don't pre-order a screening library, many vendors will offer special pricing for volume orders.

2. Virtual Vendor subsets (typically 8-10 weeks delivery).
Use these if rapid turnaround is not essential. Advantages: gives you access to over twice as many compounds as the "immediate delivery" subsets.

3. Property-filtered subsets.
We particularly favor subset #2 (fragment like) and #1 (lead like) for many reasons: solubility, sampling of chemical space / Hann complexity, fewer docking artifacts.

4. User created subsets.
These are subsets created by users, from the search results page, using the "create subsets" button. Some are also created as byproducts of DOCK Blaster runs.

5. User-uploaded subsets.
These are compounds uploaded by users. If you uploaded molecules you want to dock, this is where to go.

6. By annotation.
You may want to dock compounds that have been pre-filtered for their likelihood of binding to certain targets, based on literature reports and patents. This option is not currently supported.

7. By 2D prediction.
You may want to dock compounds that resemble actives, based on their similarity to ensembles of actives (SEA). This option is not currently supported.

= What should I dock? =
Relatively small binding site: start with "fragment like" (by property, #2). Larger binding site, start with "lead like" (by property #1).

-- John Irwin