How to use the Retrosynthesis parameters to rescore molecules during generation?

This article explains how to score generated molecules using the Retrosynthesis parameters. The Retrosynthesis parameters help you sort and prioritize your molecules for synthesis, based on your own synthetic constraints that you can specify through our large range of available search parameters. 

• Step 1: Create a new Generator

In the "Generators" tab, create a new Generator. Set it up with the parameters, constraints and rewards that are most adapted to your project. 

(If you are uncertain how to set up your generator, you can take our guided Makya setup questionnaire, or have a look at our Use-cases for inspiration!)

• Step 2: Select the Retrosynthesis parameters

1. In your generator set-up, go to the "Retrosynthesis" tab and select your parameters. Even if you have not created your own set of Retrosynthesis parameters, the Default retrosynthesis scoring is always available. 
2. Once you have finished setting up your generator, click on Run in the Generators page. All the generated molecules will be rescored using the Retrosynthesis scoring.

Note: The rescoring via our Spaya algorithm can take some time, and all the molecules will not be instantaneously rescored. Scores will keep being computed and sent to Makya for all the generated molecules, even if you stop your generation.  

Retrosynthesis score = Empty → Calculation ongoing 

Retrosynthesis score = NA → No route was found  

In the generator's result, click on the "Display Scores" icon and select the Retrosynthesis score and Retrosynthesis steps to display them in all the generated molecules.

You can sort by the Retrosynthesis score afterward.

• Step 3 (with a Spaya license): Score your list of molecules

If you have a Spaya license, by clicking on the Spaya icon on any molecule of your dataset, you can send that molecule to Spaya and open a retrosynthesis search with the exact set of search parameters you set. This allows you to see the details of the retrosynthesis route (the different steps, the starting materials, their providers, the references from the literature...):

In Spaya: