Reymond Research Group

University of Bern


Datasets and their influence on the development of computer assisted synthesis planning tools in the pharmaceutical domain

Tags: Publications

The paper Datasets and their influence on the development of computer assisted synthesis planning tools in the pharmaceutical domain has just been accepted by Chemical Science.

Computer Assisted Synthesis Planning (CASP) has gained considerable interest as of late. Herein we investigate a template-based retrosynthetic planning tool, trained on a variety of datasets consisting of up to 17.5 million reactions. We demonstrate that models trained on datasets such as internal Electronic Laboratory Notebooks (ELN), and the publicly available United States Patent Office (USPTO) extracts, are sufficient for the prediction of full synthetic routes to compounds of interest in medicinal chemistry. As such we have assessed the models on 1,731 compounds from 41 virtual libraries for which experimental results were known. Furthermore, we show that accuracy is a misleading metric for assessment of the policy network, and propose that the number of successfully applied templates, in conjunction with the overall ability to generate full synthetic routes be examined instead. To this end we found that the specificity of the templates comes at the cost of generalizability, and overall model performance. This is supplemented by a comparison of the underlying datasets and their corresponding models.

Author(s): Amol Thakkar, Thierry Kogej, Jean-Louis Reymond, Ola Engkvist and Esben Bjerrum