ZINC subsets - Revision history

Frodo at 05:28, 14 February 2014

2014-02-14T05:28:38Z

← Older revision		Revision as of 05:28, 14 February 2014
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	Some vendors offer compounds that they will make if asked, usually within about 10 weeks. We like these compounds, because they greatly expand the region of chemical space one can sample without performing synthesis oneself.		Some vendors offer compounds that they will make if asked, usually within about 10 weeks. We like these compounds, because they greatly expand the region of chemical space one can sample without performing synthesis oneself.

	~~-- John Irwin~~		[[User:Frodo]]


			[[Category:ZINC]]

Therese: 11 revisions

2012-10-08T20:33:21Z

11 revisions

← Older revision

Revision as of 20:33, 8 October 2012

Frodo at 06:04, 15 December 2011

2011-12-15T06:04:54Z

← Older revision		Revision as of 06:04, 15 December 2011
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	ZINC is big. Currently, ZINC has over ~~12M~~ molecules, about 9M of which are commercially available. For most applications, most users of ZINC will only want or need to download a fraction of ZINC: a subset. This article describes subsets.		ZINC is big. Currently, ZINC has over 20M molecules, about 14M of which are commercially available. For most applications, most users of ZINC will only want or need to download a fraction of ZINC: a subset. This article describes subsets.

	= Subset classes =		= Subset classes =
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	* immediate availability subsets, numbers 21-30. Normal subsets include compounds that are available from stock, and also compounds that can be made in 6-10 weeks. Some people only want compounds that can be obtained immediately, say less than 2 weeks. If so, this subset is for you.		* immediate availability subsets, numbers 21-30. Normal subsets include compounds that are available from stock, and also compounds that can be made in 6-10 weeks. Some people only want compounds that can be obtained immediately, say less than 2 weeks. If so, this subset is for you.

			{{TOCright}}

	= Property Subsets =		= Property Subsets =

Frodo: /* By Annotation */

2009-02-19T00:29:31Z

By Annotation

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 = By Annotation =
 We offer compounds by annotation. more soon.
 = Synthesis on Request =

Frodo at 20:37, 17 February 2009

2009-02-17T20:37:24Z

← Older revision		Revision as of 20:37, 17 February 2009
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	== drug like ==		== drug like ==
	Drug-like (#3) captures the famous rule-of-fives, which itself is just a guideline, to which there are many exceptions. There will be times you may want to screen the "drug like" subset of ZINC, but this would probably be later in the project, after you have had a good look at the leads already, or perhaps there is some unusual circumstance.		Drug-like (#3) captures the famous rule-of-fives, which itself is just a guideline, to which there are many exceptions. There will be times you may want to screen the "drug like" subset of ZINC, but this would probably be later in the project, after you have had a good look at the leads already, or perhaps there is some unusual circumstance.

	~~== greasy ==~~
	Greasy-leads (#4) and Big-n-greasy(#5) are deprecated. Frankly, these compounds are nothing but trouble, since they often do not dissolve. If you really want them back, write me, but otherwise, they are gone.

	== everything subsets ==		== everything subsets ==
	All purchasable (#6) comes in third place for popularity. Advantage: you can buy these compounds. Disadvantage: for target based virtual screening, many of these compounds will be a waste of time, because they are too big, too specific, and too greasy (insoluble).		All purchasable (#6) comes in third place for popularity. Advantage: you can buy these compounds. Disadvantage: for target based virtual screening, many of these compounds will be a waste of time, because they are too big, too specific, and too greasy (insoluble).

	~~Subsets 7,8,9 will return soon...~~

	Everything (#10) comes in fourth place for popularity, since it is, well, everything we can let you have. We frankly don't think you really want this, but people keep asking for it, so, here it is.		Everything (#10) comes in fourth place for popularity, since it is, well, everything we can let you have. We frankly don't think you really want this, but people keep asking for it, so, here it is.

			= deprecated =

			Subsets 7,8,9 will return soon...

	Subsets 11-16 will return soon....		Subsets 11-16 will return soon....

	~~== fragment variations ==~~
	Neutral-fragments (#17) are what the name suggests: uncharged fragments. Why would you want this? Charged compounds often have a hard time getting into cells. Docking programs can have trouble weighting among charged and neutral compounds. Wham - put those ideas together and you see why neutral fragments can be interesting.		Neutral-fragments (#17) are what the name suggests: uncharged fragments. Why would you want this? Charged compounds often have a hard time getting into cells. Docking programs can have trouble weighting among charged and neutral compounds. Wham - put those ideas together and you see why neutral fragments can be interesting.

	~~Subsets 18~~-~~28 will return soon.~~...		== greasy ==
			Greasy-leads (#4) and Big-n-greasy(#5) are deprecated. Frankly, these compounds are nothing but trouble, since they often do not dissolve. If you really want them back, write me, but otherwise, they are gone.

	CNS permeable (#29) are of interest for some projects where getting through the BBB is important. We have used well known criteria for this subset.		CNS permeable (#29) are of interest for some projects where getting through the BBB is important. We have used well known criteria for this subset.

Frodo at 19:09, 17 February 2009

2009-02-17T19:09:01Z

← Older revision		Revision as of 19:09, 17 February 2009
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	ZINC is big. Currently, ZINC has over 12M molecules, about 9M of which are commercially available. For most applications, most users of ZINC will only want or need to download a fraction of ZINC: a subset. This article describes subsets.		ZINC is big. Currently, ZINC has over 12M molecules, about 9M of which are commercially available. For most applications, most users of ZINC will only want or need to download a fraction of ZINC: a subset. This article describes subsets.

			= Subset classes =
			* Standard subsets, numbers 1-10. These are our approximations of popular subsets that appear commonly in the literature
			* clean subsets, numbers 11-20. Here we have removed compounds that are known to cause problems in some assays. For information about the additional filtering used, please see [http://filtering.docking.org/]
			* immediate availability subsets, numbers 21-30. Normal subsets include compounds that are available from stock, and also compounds that can be made in 6-10 weeks. Some people only want compounds that can be obtained immediately, say less than 2 weeks. If so, this subset is for you.


	= Property Subsets =		= Property Subsets =

Frodo: /* How to create a subset for docking based on SMILES */

2008-09-04T19:59:17Z

How to create a subset for docking based on SMILES

← Older revision		Revision as of 19:59, 4 September 2008
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	We offer the capability to create small subsets. You can do this via the ZINC results browser page after a search by clicking on "create subset". Another way, if you have the SMILES, to generate a custom subset, is to upload the molecules.		We offer the capability to create small subsets. You can do this via the ZINC results browser page after a search by clicking on "create subset". Another way, if you have the SMILES, to generate a custom subset, is to upload the molecules.

	= How to create a subset for docking based on SMILES =		== How to create a subset for docking based on SMILES ==
	* 1. Browse to the upload page, http://zinc.docking.org/upload.shtml		* 1. Browse to the upload page, http://zinc.docking.org/upload.shtml
	* 2. select your files with one smiles and optional identifier separated by whitespace per line		* 2. select your files with one smiles and optional identifier separated by whitespace per line

Frodo: /* User-created subsets of mini subsets */

2008-09-04T19:58:53Z

User-created subsets of mini subsets

← Older revision		Revision as of 19:58, 4 September 2008
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	= User-created subsets of mini subsets =		= User-created subsets of mini subsets =
	We offer the capability to create small subsets.		We offer the capability to create small subsets. You can do this via the ZINC results browser page after a search by clicking on "create subset". Another way, if you have the SMILES, to generate a custom subset, is to upload the molecules.

			= How to create a subset for docking based on SMILES =
			* 1. Browse to the upload page, http://zinc.docking.org/upload.shtml
			* 2. select your files with one smiles and optional identifier separated by whitespace per line
			* 3. Check box "click here if private (UCSF only)". This gives you the right to upload 5000 instead of 1000 molecules per transaction. If you are not inside UCSF or otherwise "special", you are stuck at 1000.
			* 4. Click "upload and build"
			* 5. Click on the link where it says "browse results here" (should be a number)
			* 6. Wait about 10 min per 1000 molecules (refresh page) until you see "e_0.0.db.gz" - this is the pH 7 representation of your compounds. e_1.0.db.gz is the "additional forms pH 5.75 - 8.25" file. you need to download/copy these files and dock them.
			* 7. OR, you can do: md4db.csh uploads 44249 (or whatever your number was) and it will copy them and set up for docking. (UCSF only). md4db.csh == make database for dock blaster
			* 8. Now do cd run.u44249
			* 9. Now do startdockbks3 `pwd` on sgehead to start docking.

	= User-uploaded subsets =		= User-uploaded subsets =

Frodo: /* fragment variations */

2008-07-01T23:35:34Z

fragment variations

← Older revision		Revision as of 23:35, 1 July 2008
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	== fragment variations ==		== fragment variations ==
	Neutral-fragments (#17) are what the name suggests: uncharged fragments. Why would you want this? Charged compounds often have time getting into cells. Docking programs can have trouble weighting among charged and neutral compounds. Wham - put those ideas together and you see why neutral fragments can be interesting.		Neutral-fragments (#17) are what the name suggests: uncharged fragments. Why would you want this? Charged compounds often have a hard time getting into cells. Docking programs can have trouble weighting among charged and neutral compounds. Wham - put those ideas together and you see why neutral fragments can be interesting.

	Subsets 18-28 will return soon....		Subsets 18-28 will return soon....
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	Monoanions (#31) and monocations (#32) - don't know why you would want this. We created this for a particular project.		Monoanions (#31) and monocations (#32) - don't know why you would want this. We created this for a particular project.

	Goldilocks (#33) are yet another set that try to "shoot for the middle" of the chemical space problem and balance the competing advantages and disadvantages of bigger vs smaller molecules.		Goldilocks (#33) are yet another set that try to "shoot for the middle" of the chemical space problem and balance the competing advantages and disadvantages of bigger vs smaller molecules.

	== personal subsets ==		== personal subsets ==

Frodo: /* fragment like */

2008-07-01T23:33:33Z

fragment like

← Older revision		Revision as of 23:33, 1 July 2008
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	==fragment like==		==fragment like==
	Fragment-like compounds are even smaller than leads. The good news is, they sample chemical space more throughly ~~that~~ is possible with leads. The bad news is, they are often too small to be detected in a cheap assay, requiring direct biophysical measurement, such as SPR, NMR, or X-ray crystallography.		Fragment-like compounds are even smaller than leads. The good news is, they sample chemical space more throughly than is possible with leads. The bad news is, they are often too small to be detected in a cheap assay, requiring direct biophysical measurement, such as SPR, NMR, or X-ray crystallography.

	Together, leads and fragments represent the dominant thinking in the field for screening. The remaining subsets can also be interesting. Here we give a brief explanation of why you might want each one.		Together, leads and fragments represent the dominant thinking in the field for screening. The remaining subsets can also be interesting. Here we give a brief explanation of why you might want each one.

	== drug like ==		== drug like ==