User Guide for the READRetro website

This guide provides comprehensive instructions for using all features and options available on the READRetro web interface (https://readretro.net). The official code repository for the web interface is https://github.com/pnucolab/readretro-website.

Viewing and Interpreting Results

Once a prediction job is complete, the “Result Page” will display the findings. This page is designed for clear visualization and interaction.

  • Pathway Visualization (Arrows)

    Arrows connect compounds in the predicted pathways and are color-coded to indicate the source of the prediction:

    • Red Arrows: Represent steps generated by the READRetro deep learning models (i.e., novel predictions not found directly in the retrieval databases). This is the default for a predicted transformation.

    • Blue Arrows: Indicate that the specific single-step retrosynthetic reaction was found in and retrieved from the “Reaction Retriever” database.

    • Green Arrows: Signify that a sequence of reactions (a partial or full pathway) was retrieved by the “Pathway Retriever,” often from KEGG.

  • Information Displayed with Arrows

    Additional biochemical context is provided above and below each arrow:

    • EC Numbers: Enzyme Commission numbers are displayed, classifying the potential enzymes that might catalyze the reaction. These are often clickable, linking to the BRENDA Enzyme Database for detailed enzyme information.

    • KEGG Pathway Information: If applicable, links or identifiers for relevant KEGG pathways are shown, allowing users to explore the broader biological context. These typically link to the KEGG PATHWAY database.

  • Compound Representation (Cards)

    Each molecule in the pathway is shown as an interactive card with the following features and color-coding:

    • Default Card Color: Typically red (or a neutral color) for newly predicted intermediates.

    • Blue Card Color: Indicates that the molecule is a known compound found in the KEGG COMPOUND database.

    • Yellow Card Color: Applied when a user clicks on a compound card to highlight it, making it easier to trace its involvement across different suggested pathways.

    • Information on Cards:

      • SMILES Notation: The SMILES string of the compound.

      • KEGG Entry: If the compound is in KEGG, its KEGG ID is displayed and is clickable, redirecting to the specific entry in the KEGG COMPOUND database.

      • Structural Diagram: A 2D chemical structure image of the molecule.

  • Interactive Features

    The Result Page offers several tools to aid in analysis:

    • Highlighting Compounds: Clicking on a compound card will highlight that compound across all displayed pathways.

    • Changing Pathway Display Direction: Options may be available to view pathways in the retrosynthetic (product to precursors) or biosynthetic (precursors to product) direction.

  • Saving and Re-accessing Results

    You can save and revisit your prediction results:

    • Unique Result Link: Each prediction generates a unique web link. The link follows the format https://readretro.net/result/ followed by your specific [job id] (e.g., https://readretro.net/result/d0bc0da8ebb245bb87e8aa161fbbd2d6). You can bookmark or share this link to access the specific result page again later.

    • Download Result Button: A “Download result” button allows you to download the predicted pathway information as a .txt file for offline storage, sharing, or further analysis.