Makya algorithm is chemistry-driven and will combine starting materials specified by the user with commercially available building blocks using organic chemistry reactions.
For this reason, an exit vector needs to be a reactive center that includes all the atoms involved in the reaction.
When you select an exit vector, the selected atoms are highlighted in red. For instance, if you want to react on an acid moiety to obtain an amid, the template should include the OH and the C of the acid:
If you want to react on the OH only to generate ester for instance, only the OH should be selected:
Using Spaya to find good exit vectors
Spaya is Iktos AI platform for retrosynthesis analysis. Just like Makya, it is chemistry-driven and was trained on millions of chemical reactions. As a result, using synthetic routes information from Spaya helps Makya converge towards good molecules.
The diagram below depicts an example of how you can use Spaya to find good exit vectors: a user wanting to do scaffold hopping from the reference molecule on the left can find a synthetic route for that molecule in Spaya, which gives them suitable starting materials for fragment expansion or linking.
For a Spaya demonstration, please contact your regional Application Scientist team.