AB3 - Revision history

Mtsukanov at 18:34, 21 March 2023

2023-03-21T18:34:42Z

← Older revision		Revision as of 18:34, 21 March 2023
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	Analog By Building Block (AB3~~) has two different implementations~~.		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.

	~~== interactive tool ==~~
	~~Currently available internally only at n-9-38:5000~~

	~~This tool allows you to~~		== Procedure ==
	* ~~figure out what~~ reactions ~~can produce a target~~ molecule		* Step 1. The target molecule is retrosynthesized through standard, robust reactions to separate the molecule into building blocks.
	* figure out how many analogs of each synthon are commercially available
	* build a trial library of analogs

	~~== asynchronous tool ==~~		* 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.
	~~Currently~~ available ~~internally via tldr via~~ the ~~a3b tool~~.

	~~This tools allows you to determine which reactions could produce your target compound~~.		* Step 3. The new building blocks are "reacted" in silico using the forward reaction to create a library of analogs.
	* it lists available building blocks ~~at various purchasabilities and allows you to select which ones you want to use.~~
	* it allows you to ~~generate~~ a library.

	The ~~final~~ library can be downloaded. ~~Alternately, you may route it for~~		* Step 4. The enumerated library can be downloaded, or "Published" using our tools.
	* ZINC ID
	* tranching
	* 3D building
	* distribution (FTP etc)
	* arthor and smallworld indexing

	~~You may also route~~ the ~~new library for novelty analysis property characterization etc~~.		The ABBB process is available in two separate ways: a) via TLDR and b) interactively via the AB3 tool at ab3.docking.org.

	[[Category:~~TLDR~~]]
			== 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.


			[[Category:Analogs]]

Mtsukanov at 18:08, 1 November 2022

2022-11-01T18:08:49Z

← Older revision		Revision as of 18:08, 1 November 2022
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	== interactive tool ==		== interactive tool ==
	~~currently~~ available internally only at n-9-38:5000		Currently available internally only at n-9-38:5000

	This tool allows you to		This tool allows you to
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	== asynchronous tool ==		== asynchronous tool ==
	~~currently~~ available internally via tldr via the a3b tool.		Currently available internally via tldr via the a3b tool.

	This tools allows you to determine which reactions could produce your target compound.		This tools allows you to determine which reactions could produce your target compound.

Frodo: asdf

2022-08-18T00:15:03Z

asdf

New page

Analog By Building Block (AB3) has two different implementations.

== interactive tool ==
currently available internally only at n-9-38:5000

This tool allows you to
* figure out what reactions can produce a target molecule
* figure out how many analogs of each synthon are commercially available
* build a trial library of analogs

== asynchronous tool ==
currently available internally via tldr via the a3b tool.

This tools allows you to determine which reactions could produce your target compound.
* it lists available building blocks at various purchasabilities and allows you to select which ones you want to use.
* it allows you to generate a library.

The final library can be downloaded. Alternately, you may route it for
* ZINC ID
* tranching
* 3D building
* distribution (FTP etc)
* arthor and smallworld indexing

You may also route the new library for novelty analysis property characterization etc.

[[Category:TLDR]]