ZINC Biogenic Libraries: Difference between revisions
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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. | |||
= Assembly = | = Assembly = |
Revision as of 01:51, 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. These libraries are 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. We are also inspired by the Dortmund and Broad/Harvard groups working in the areas of natural products and nature-inspired compounds.
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.