ZINC Biogenic Libraries: Difference between revisions
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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 | 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 = | ||
* 1. | * 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. | * 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. | ||
= Results = | = Results = | ||
* organized into lead-like, fragment-like, drug-like, all, and shard-like subsets, for both biogenic and biogenic like. | * 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 = | ||
Hert, Dortmund Group, Broad/Harvard Group. | |||
[[Category:ZINC]] | [[Category:ZINC]] | ||
Revision as of 01:50, 25 February 2013
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.
Inspired by the argument in Hert et al NCB 2008, we then find all compounds that are similar to these biogenic molecules for the biogenic-like libraries.
Assembly
- 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.
- 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.
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.
Inspiration
Hert, Dortmund Group, Broad/Harvard Group.