ReactionViewer Datasets

Computer-readable generic reaction schemes are a fundamental technique in the in silico drug design process. Due to their complexity and the richness of features represented in a single line, they can be challenging to work with even for experienced users. To generate a visualization of generic reaction patterns written as Reaction SMILES, Reaction SMARTS or in the SMIRKS language, we developed a novel method, called ReactionViewer.[1] The ReactionViewer is based on the SMARTScompareViewer[2] and integrated into our web frontend https://smarts.plus.

In the following, we provide the visualization of two datasets of reaction schemes for organic synthesis from recent publications. We provide a complete visualization of all given reaction schemes for both datasets:

• The first dataset comes from an open-source retrosynthetic planning software called AiZynthFinder.[3] The tool is available with a set of reaction schemes used for the neural network policy training, among others. The reaction dataset is based on the publicly available US patent office data. The 46,696 reaction schemes are written in a retrosynthetic manner.
  https://amd.zbh.uni-hamburg.de/download/amd/AiZynthFinder_Dataset_Visualization.pdf
• The second data set is extracted from Hartenfeller et al.[4], who provided a set of robust organic reaction schemes available for in silico molecule design. The 58 reaction schemes are written in a forward synthetic manner.
  https://www.zbh.uni-hamburg.de/forschung/amd/datasets/reaction-viewer-datasets/hartenfeller-dataset-visualization-v2.pdf

[1] Dolfus, U.; Briem, H.; Rarey, M. Visualizing Generic Reaction Patterns. J Chem Inf Model 2022, 62 (19), 4680-4689. DOI: https://doi.org/10.1021/acs.jcim.2c00992
[2] Schomburg, K.; Ehrlich, H. C.; Stierand, K.; Rarey, M. From Structure Diagrams to Visual Chemical Patterns. J Chem Inf Model 2010, 50 (9), 1529-1535. DOI: https://doi.org/10.1021/ci100209a
[3] Genheden, S.; Thakkar, A.; Chadimova, V.; Reymond, J. L.; Engkvist, O.; Bjerrum, E. AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning. J Cheminform 2020, 12 (1), 70. DOI: https://doi.org/10.1186/s13321-020-00472-1
{4] Hartenfeller, M.; Eberle, M.; Meier, P.; Nieto-Oberhuber, C.; Altmann, K. H.; Schneider, G.; Jacoby, E.; Renner, S. A collection of robust organic synthesis reactions for in silico molecule design. J Chem Inf Model 2011, 51 (12), 3093-3098. DOI: https://doi.org/10.1021/ci200379p