ZINC Biogenic Libraries - Revision history

Frodo at 15:28, 11 March 2014

2014-03-11T15:28:19Z

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	[[Category:ZINC]]		[[Category:ZINC]]
			[[Category:Natural products]]
			[[Category:Databases]]

Frodo: /* Results */

2013-02-27T01:39:59Z

Results

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	= Results =		= Results =
	* Subsets are organized into lead-like, fragment-like, drug-like, all, and shard-like subsets as usual, for both biogenic and biogenic like. These are called Zbc - ZINC Biogenic compounds and Zni - ZINC Nature Inspired. We made these names deliberately different for clarity. Zbc compounds are produced by nature, and nature has been seeing them for evolutionary time. Zni - nature inspired - include both compounds from nature and synthetic compounds that look natural, when you have your Tanimoto 80% glasses on.		Subsets are organized into lead-like, fragment-like, drug-like, all, and shard-like subsets as usual, for both biogenic and biogenic like. These are called Zbc - ZINC Biogenic compounds and Zni - ZINC Nature Inspired. We made these names deliberately different for clarity. Zbc compounds are produced by nature, and nature has been seeing them for evolutionary time. Zni - nature inspired - include both compounds from nature and synthetic compounds that look natural, when you have your Tanimoto 80% glasses on.

	= Inspiration =		= Inspiration =

Frodo: /* Argument */

2013-02-27T01:39:48Z

Argument

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	= Argument =		= Argument =
	The argument is that nature-like biased screening libraries should provide far richer and denser hits that one would expect by screening synthetic compounds alone. Indeed, the only reason HTS and virtual screening work as well as they do is that they are already heavily biased towards biogenic like molecules.		The argument is that nature-like biased screening libraries should provide far richer and denser hits that one would expect by screening synthetic compounds alone. Indeed, the only reason HTS and virtual screening work as well as they do is that they are already heavily biased towards biogenic like molecules. These may also be good for protein function identification via docking, because if a site recognizes a molecule from nature, then perhaps that or a similar one is the endogenous ligand for that site.

	[[Category:ZINC]]		[[Category:ZINC]]

Frodo: /* Results */

2013-02-27T01:38:30Z

Results

← Older revision		Revision as of 01:38, 27 February 2013
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	= Results =		= Results =
	* Subsets are organized into lead-like, fragment-like, drug-like, all, and shard-like subsets as usual, for both biogenic and biogenic like. These are called Zbc - ZINC Biogenic compounds and Zni - ZINC Nature Inspired. We made these names deliberately different for clarity. Zbc compounds are produced by nature, and nature has been seeing them for evolutionary time. Zni - nature inspired - include both ~~natural~~ and compounds that look natural, when you have your Tanimoto 80% glasses on.		* Subsets are organized into lead-like, fragment-like, drug-like, all, and shard-like subsets as usual, for both biogenic and biogenic like. These are called Zbc - ZINC Biogenic compounds and Zni - ZINC Nature Inspired. We made these names deliberately different for clarity. Zbc compounds are produced by nature, and nature has been seeing them for evolutionary time. Zni - nature inspired - include both compounds from nature and synthetic compounds that look natural, when you have your Tanimoto 80% glasses on.

	= Inspiration =		= Inspiration =

Frodo at 01:30, 27 February 2013

2013-02-27T01:30:31Z

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	Biogenic and Biogenic-like libraries in ZINC.		Biogenic and Biogenic-like libraries in ZINC.

	We have created screening libraries based on molecules of biological origin. To be clear, we include both primary metabolites - often just called metabolites - as well as secondary metabolites - often called natural products - in our database of biogenic molecules. These libraries are inspired by the argument in [http://zinc.docking.org/browse/subsets/special \|Hert et al NCB 2008], we then find all compounds that are similar to these biogenic molecules for the biogenic-like libraries. We are also inspired by the Dortmund and Broad/Harvard groups working in the areas of natural products and nature-inspired compounds.		We have created screening libraries based on molecules of biological origin. To be clear, we include both primary metabolites - often just called metabolites - as well as secondary metabolites - often called natural products - in our database of biogenic molecules. These libraries are inspired by the argument in [http://zinc.docking.org/browse/subsets/special Hert et al NCB 2008], we then find all compounds that are similar to these biogenic molecules for the biogenic-like libraries. We are also inspired by the Dortmund and Broad/Harvard groups working in the areas of natural products and nature-inspired compounds.

	= Assembly =		= Assembly =

Frodo at 01:55, 25 February 2013

2013-02-25T01:55:27Z

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	= Inspiration =		= Inspiration =
	Hert, Dortmund Group, Broad/Harvard Group.		Hert, Dortmund Group, Broad/Harvard Group.

			= Argument =
			The argument is that nature-like biased screening libraries should provide far richer and denser hits that one would expect by screening synthetic compounds alone. Indeed, the only reason HTS and virtual screening work as well as they do is that they are already heavily biased towards biogenic like molecules.

	[[Category:ZINC]]		[[Category:ZINC]]

Frodo at 01:53, 25 February 2013

2013-02-25T01:53:40Z

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	= Assembly =		= Assembly =
	* 1. All biogenic compounds from public sources. The purchasable version of this is subset 98. Zbc - ZINC Biogenic compounds.		* 1. All biogenic compounds from public sources. The purchasable version of this is subset 98. Zbc - ZINC Biogenic compounds.
	* 2. Tanimoto 80% similarity to any Biogenic compound, based on rdkit path-based fingerprints, 2048 bits.		* 2. Tanimoto 80% similarity or better to any Biogenic compound, based on rdkit path-based fingerprints, 2048 bits.
	* 3. We fragment Biogenic compounds into Murcko Scaffolds and ring systems (Ertl, via molinspiration. type 2 and 3 fragmentation). We retain only ring systems of 10 or more atoms and ~~compute~~ Tanimoto 80% similarity (rdkit 2048 pathbased) to any Biogenic fragment thus calculated.		* 3. We fragment Biogenic compounds into Murcko Scaffolds and ring systems (Ertl, via molinspiration. type 2 and 3 fragmentation). We retain only ring systems of 10 or more atoms and then accept compounds having Tanimoto 80% similarity or better (rdkit 2048 pathbased) to any Biogenic 10+ atom fragment thus calculated.

	= Results =		= Results =

Frodo at 01:51, 25 February 2013

2013-02-25T01:51:57Z

← Older revision		Revision as of 01:51, 25 February 2013
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	Biogenic and Biogenic-like libraries in ZINC.		Biogenic and Biogenic-like libraries in ZINC.

			We have created screening libraries based on molecules of biological origin. To be clear, we include both primary metabolites - often just called metabolites - as well as secondary metabolites - often called natural products - in our database of biogenic molecules. These libraries are inspired by the argument in [http://zinc.docking.org/browse/subsets/special \|Hert et al NCB 2008], we then find all compounds that are similar to these biogenic molecules for the biogenic-like libraries. We are also inspired by the Dortmund and Broad/Harvard groups working in the areas of natural products and nature-inspired compounds.
	We have created screening libraries based on molecules of biological origin.
	To be clear, we include both primary metabolites - often just called metabolites - as well as secondary metabolites - often called natural products - in our database of biogenic molecules.

	~~Inspired~~ by the argument in [http://zinc.docking.org/browse/subsets/special Hert et al NCB 2008], we then find all compounds that are similar to these biogenic molecules for the biogenic-like libraries.

	= Assembly =		= Assembly =

Frodo at 01:50, 25 February 2013

2013-02-25T01:50:24Z

← Older revision		Revision as of 01:50, 25 February 2013
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	We have created screening libraries based on molecules of biological origin.		We have created screening libraries based on molecules of biological origin.
	To be clear, we include both primary metabolites - often just called metabolites - as well as secondary metabolites - often called natural products - in our database of ~~natural products~~.		To be clear, we include both primary metabolites - often just called metabolites - as well as secondary metabolites - often called natural products - in our database of biogenic molecules.

	~~Based on~~ Hert et al ~~2006~~, we then find all compounds that are similar to these biogenic molecules for the ~~natural product~~ like libraries.		Inspired by the argument in [http://zinc.docking.org/browse/subsets/special Hert et al NCB 2008], we then find all compounds that are similar to these biogenic molecules for the biogenic-like libraries.

	= Assembly =		= Assembly =
	* 1. ~~all natural products~~ from public sources. The purchasable version of this is subset 98. ~~ZBS~~ - ZINC Biogenic ~~Subset~~		* 1. All biogenic compounds from public sources. The purchasable version of this is subset 98. Zbc - ZINC Biogenic compounds.
	* 2. Tanimoto 80% similarity to any Biogenic compound, based on rdkit path-based fingerprints, 2048 bits.		* 2. Tanimoto 80% similarity to any Biogenic compound, based on rdkit path-based fingerprints, 2048 bits.
	* 3. ~~Fragment~~ Biogenic compounds into Murcko Scaffolds and ring systems (Ertl, via molinspiration). ~~Retain~~ only 10~~+ atom fragments.~~		* 3. We fragment Biogenic compounds into Murcko Scaffolds and ring systems (Ertl, via molinspiration. type 2 and 3 fragmentation). We retain only ring systems of 10 or more atoms and compute Tanimoto 80% similarity (rdkit 2048 pathbased) to any Biogenic fragment thus calculated.
	* 3a. Tanimoto 80% similarity (rdkit 2048 pathbased) to any Biogenic fragment ~~in 3 above.~~
	* 3b. Any compound having as a strict substructure the fragments in 3 above.

	= Results =		= Results =
	* organized into lead-like, fragment-like, drug-like, all, and shard-like subsets, for both biogenic and biogenic like. ~~Called ZBG~~ - ZINC ~~BioGenic~~ and ~~ZBL~~ - ZINC ~~Biogenic Like subsets~~.		* Subsets are organized into lead-like, fragment-like, drug-like, all, and shard-like subsets as usual, for both biogenic and biogenic like. These are called Zbc - ZINC Biogenic compounds and Zni - ZINC Nature Inspired. We made these names deliberately different for clarity. Zbc compounds are produced by nature, and nature has been seeing them for evolutionary time. Zni - nature inspired - include both natural and compounds that look natural, when you have your Tanimoto 80% glasses on.

	= Inspiration =		= Inspiration =
	~~inspired by the work of~~ Hert ~~et la.~~		Hert, Dortmund Group, Broad/Harvard Group.
	~~Also~~ Dortmund Group.
	~~Also Reses paper~~.

	[[Category:ZINC]]		[[Category:ZINC]]

Frodo: Frodo moved page ZINC Natural Product Like Library to ZINC Biogenic Libraries

2013-02-22T05:49:33Z

Frodo moved page ZINC Natural Product Like Library to ZINC Biogenic Libraries

← Older revision

Revision as of 05:49, 22 February 2013