ZINC Biogenic Libraries: Difference between revisions
Jump to navigation
Jump to search
(Created page with "The ZINC Natural Product Like library is a collection of commercially available compounds that are natural products, strongly ressemble natural products, or have signifcant su...") |
No edit summary |
||
| Line 1: | Line 1: | ||
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 natural products. | |||
Based on Hert et al 2006, we then find all compounds that are similar to these biogenic molecules for the natural product like libraries. | |||
= Assembly = | = Assembly = | ||
* 1. | * 1. all natural products from public sources. The purchasable version of this is subset 98. ZBS - ZINC Biogenic Subset | ||
* 2. Tanimoto 80% similarity to any | * 2. Tanimoto 80% similarity to any Biogenic compound, based on rdkit path-based fingerprints, 2048 bits. | ||
* 3. Fragment | * 3. Fragment Biogenic compounds into Murcko Scaffolds and ring systems (Ertl, via molinspiration). Retain only 10+ atom fragments. | ||
* 3a. Tanimoto 80% similarity to any | * 3a. Tanimoto 80% similarity (rdkit 2048 pathbased) to any Biogenic fragment in 3 above. | ||
* 3b. | * 3b. Any compound having as a strict substructure the fragments in 3 above. | ||
= 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. | |||
= Inspiration = | = Inspiration = | ||
Revision as of 05:49, 22 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 natural products.
Based on Hert et al 2006, we then find all compounds that are similar to these biogenic molecules for the natural product like libraries.
Assembly
- 1. all natural products from public sources. The purchasable version of this is subset 98. ZBS - ZINC Biogenic Subset
- 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.
- 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
- 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.
Inspiration
inspired by the work of Hert et la. Also Dortmund Group. Also Reses paper.