ABBB
ABBB or Analog by Building Block also called AB3 is a tool for finding analogs that are accessible from commercially available building blocks. During development it is at n-9-38:5005. When it goes to production it will appear at ab3.docking.org.
Procedure
- Step 1. The target molecule is retrosynthesized through standard, robust reactions to separate the molecule into building blocks.
- Step 2. Commercially available analogs of the building blocks are found by similarity search using Arthor, and filtered against must-not-have rules for each reaction, respectively.
- Step 3. The new building blocks are "reacted" in silico using the forward reaction to create a library of analogs.
- Step 4. The enumerated library can be downloaded, or "Published" using our tools.
The ABBB process is available in two separate ways: a) via TLDR and b) interactively via the AB3 tool at n-9-38:5005.
Batch version
The batch version in TLDR is broken up into modules. The first module called "a3B" takes an input of the list of molecules through a text file and a desired Tanimoto coefficient. You can also add your inclusion and exclusion SMARTS. The module then take the inputs and outputs a list of building blocks that are generated through retrosynthesis and then a similarity search using the tanimoto coefficients.
Interactive version
The interactive version of the tool can be accessed at the ABBB.docking.org(soon to come!). It is a simple version that can only do one molecule at a time and won't output as many results as the batch version can. The tool is made to be as simple as it possibly can. The tool takes in an input of the molecule through a drawing function or a SMILES pattern and also the Tanimoto coefficient for the building blocks and outputs a list of analogs.
Any inputs of additional reaction SMARTS patterns can be requested by emailing mtsukanov at berkeley dot edu. Send in a list of working reaction SMARTS and he will do his best to implement them as quickly as possible into both of the version of the ABBB tools.