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Figure 1. SQL schema used by RetroRules

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1 Figure 1. SQL schema used by RetroRules
Figure 1. SQL schema used by RetroRules. The tables in white are the parsed meta-information from various datasets and ... Figure 1. SQL schema used by RetroRules. The tables in white are the parsed meta-information from various datasets and their cross-references to others databases. The reactions and chemical_species tables are linked together through the bridge tables reaction_products and reaction_substrates. In blue are the tables associated with reaction rules. The rules table uniquely identifies a given rule with single reaction_id and substrate_id at a given diameter. The isStereo parameter determines if the rule describes the stereochemistry of the reaction or not. Each rule is associated with a single SMARTS and SMILES description of that reaction, and to link the two, a smarts_smiles table assures that one is able to easily find the corresponding SMILES description of a SMARTS and vice-versa. The rule_products table describes the products of a given rule. Lastly in yellow are the tables that were used to generate the score (also in yellow in the rules table) from the rules table (see the Reaction rule scoring section). Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, Volume 47, Issue D1, 13 October 2018, Pages D1229–D1235, The content of this slide may be subject to copyright: please see the slide notes for details.

2 Figure 2. Calculation of reaction rules for EC 2. 6. 1. 5
Figure 2. Calculation of reaction rules for EC (A) The atom mapping highlights reacting atoms labelled 8, 11, ... Figure 2. Calculation of reaction rules for EC (A) The atom mapping highlights reacting atoms labelled 8, 11, 16 and 19. (B) Calculation of the EC rules for diameters D = ∞, 4 and 0 modeling promiscuity on substrate 4-hydroxyphenylpyruvate. (C) Calculation of the EC rules for diameters D = ∞, 4 and 0 modelling promiscuity on substrate l-glutamate. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, Volume 47, Issue D1, 13 October 2018, Pages D1229–D1235, The content of this slide may be subject to copyright: please see the slide notes for details.

3 Figure 3. Reaction rules querying process from the RetroRules web interface using as entry point EC number Figure 3. Reaction rules querying process from the RetroRules web interface using as entry point EC number (chalcone–flavanone isomerase) and minimum diameter d = 6. (A) Home page is the go-to page to start a search for specific reactions and associated rules using EC number, reaction ID, substrate name of structure query. (B) Reaction rules matching queries are ranked according to their score in tables that may be exported as CSV or JSON for downstream programmatic analysis. (C) Each rule can be further investigated from contextual information such as associated reactions and enzyme sequences using the single reaction rule view. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, Volume 47, Issue D1, 13 October 2018, Pages D1229–D1235, The content of this slide may be subject to copyright: please see the slide notes for details.

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