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Updated: Aug 16, 2025

A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
Guided discovery of chemical reaction pathways with imposed activation
Cyrille Lavigne1, Gabe Gomes1,2, Robert Pollice1,2
1Department of Computer Science, University of Toronto 214 College St. Toronto Ontario M5T 3A1 Canada gabegomes@cmu.edu r.pollice@rug.nl aspuru@utoronto.ca.
Abstract:
Computational power and quantum chemical methods have improved immensely since computers were first applied to the study of reactivity, but the de novo prediction of chemical reactions has remained challenging. We show that complex reaction pathways can be efficiently predicted in a guided manner using chemical activation imposed by geometrical constraints of specific reactive modes, which we term imposed activation (IACTA). Our approach is demonstrated on realistic and challenging chemistry, such as a triple cyclization cascade involved in the total synthesis of a natural product, a water-mediated Michael addition, and several oxidative addition reactions of complex drug-like molecules. Notably and in contrast with traditional hand-guided computational chemistry calculations, our method requires minimal human involvement and no prior knowledge of the products or the associated mechanisms. We believe that IACTA will be a transformational tool to screen for chemical reactivity and to study both by-product formation and decomposition pathways in a guided way.
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