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ABBB or Analog By Building Block is a tool designed by the Irwin Lab for the purpose of analogizing molecules. The molecules that are given to the tool are first retrosynthesized through robust reactions to separate the molecule into building blocks. Similar building blocks to the ones derived can then be found through a similarity search and filter through Arthor. Those new building blocks can then be recombined through the forward synthesis of the same reaction used to break apart the molecules. The resulting molecules will be analogs of the molecules that were given to the tool. The molecules can then be enumerated into a library.
ABBB or Analog by Building Block also called AB3 is a tool for finding analogs that are accessible from commercially available building blocks.  Currently, it can be accessed 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 ab3.docking.org.  


The tool can be accessed in two ways: One is a batch version of the tool through TLDR and the second is a compact interactive tool version called ABBB.


== Batch version ==
== 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.
The batch version in TLDR is broken up into modules. The first module called "retrosynthesis" takes an input of the list of molecules through a text file and runs these molecule through retrosynthetic reactions to produce building blocks. The second module called "enumeration" takes an input of the list of building blocks along with a desired tanimoto coefficient and runs them through arthor's similarity search to generate a list of building block analogs. You can also add your inclusion and exclusion SMARTS.  


== Interactive version ==
== 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.  
The interactive version of the tool can be accessed at the ab3.docking.org. 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.
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.
[[Category:Analogs]]

Latest revision as of 18:46, 4 November 2022

ABBB or Analog by Building Block also called AB3 is a tool for finding analogs that are accessible from commercially available building blocks. Currently, it can be accessed 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 ab3.docking.org.


Batch version

The batch version in TLDR is broken up into modules. The first module called "retrosynthesis" takes an input of the list of molecules through a text file and runs these molecule through retrosynthetic reactions to produce building blocks. The second module called "enumeration" takes an input of the list of building blocks along with a desired tanimoto coefficient and runs them through arthor's similarity search to generate a list of building block analogs. You can also add your inclusion and exclusion SMARTS.

Interactive version

The interactive version of the tool can be accessed at the ab3.docking.org. 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.

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