There are two main approaches to drawing reactions: the canvas model, where everything is drawn onto a flat page, and the component model, where each reaction participant is treated as a discrete object. Both of these approaches have important advantages, and significant problems which have to be addressed.
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Reaction Prediction Models: Chapter 8 – Aligned Depiction
Sometimes the world of informatics overlaps strongly with the universe of human comprehension, and reaction component alignment is one of these cases: when reactants and products are drawn with a common orientation, it can be made very easy and immediately apparent to anyone with basic chemistry experience what is going on in the reaction. An arbitrary molecule layout on the other hand can impose a fairly high cognitive burden.
Continue readingReaction Prediction Models: Chapter 7 – Backward/Forward Synthesis and Reagents
Using models to propose recommendations for chemical reactions is appropriate for many of the steps needed to fill out the scheme, but sometimes it’s more effective to pick an existing reaction and use it as a template to build out the missing pieces. This approach can be applied to forward and backward syntheses (starting from a reactant or product respectively) and also to finding and proposing stoichiometric reagents.
Continue readingReaction Prediction Models: Chapter 2 – Solvents
In this chapter we will explore models that can propose and rank solvents for a partially specified reaction. The methodology uses graph-based deep learning models trained on a moderate sized corpus of very well curated reactions with each of the solvents represented as a chemical structure.
Continue readingReaction Prediction Models: Chapter 1 – Catalysts
In this chapter we will explore models that can propose and rank catalysts for a given reaction transform. The methodology uses graph-based deep learning models trained on a moderate sized corpus of very well curated reactions, each of which has the catalyst molecule (or set of molecules) drawn with a chemically meaningful structure.
Continue readingReaction Prediction Models: Chapter 0
This is the first article in a series about chemical reaction prediction, in particular a work-in-progress site that combines a number of original tools for designing reactions. The general idea is that you start with an incomplete reaction scheme, and the models and algorithms will guide you toward filling out the rest, so you end up with a useful starting point for an actual experiment.
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Cheminformatics 2.0 