Shared Path Libraries

Shared Path Libraries results are presented in a modified Pathway View. Each pathway is presented as a reaction scheme from starting materials to target compound. The reaction name and typical conditions are shown above each reaction arrow. Links for illustrative references are displayed under the reaction arrow for reactions originated from published reaction databases. Price per gram is displayed below the structure of commercially available compounds.

Additional tags provide further information on compounds and reactions. See the “Path View Legend” section for more details.

>> Path View

The number of compounds in the library is displayed next to the library name, at the top of the results. Click on the Eye icon to see the structures of the target molecules in a popup window. 

When a library molecule is structurally too different from the rest of the library, SYNTHIA™ may not be able to find shared reactions or intermediates for it. In this case, this molecule is not included in the results. You can see which molecules have been excluded in the target molecules popup window.

For Shared Path Libraries, SYNTHIA™ returns three sets of pathways per library. Each set contains one pathway for each target molecule and highlights shared intermediates and reactions between the pathways in the set.

Each set is assigned a set rank number, starting from 1. Set rank can be found on top of each set, in their lavender header. The number of unique reactions and repeated intermediates for all the pathways in the set is also displayed next to the set rank.

Starting materials and intermediates that are common to multiple pathways in a set are highlighted in a matching color box in each pathway. The badge on the box indicates the number of pathways which use the molecule in the set.

Similarly, reactions that are repeated in multiple pathways in a set are highlighted with matching color arrows, with a badge indicating the number of pathways which use the reaction in the set.

Use the up/down arrow at the bottom of the pathway to resize the window height. Double click on a white space close to a reaction to zoom in to the reaction details. Double click a second time in any white space to zoom out and see the whole pathway. You can also move the reaction scheme using your mouse to drag it in any direction or use your mouse wheel to zoom in and out. Click on any molecule or a reaction name to open their molecule or reaction card. (See “Molecule Cards” or “Reaction Cards” for more details.) 

>> Molecule Cards
>> Reaction Cards

Click the Expanded Path View icon, at the top right of each pathway to open Expanded Path View. Expanded Path View gives you a close-up detailed view of one individual pathway.

Path rank for each target molecule is listed on the upper left of the screen. As in Pathway View, you can move the reaction scheme using your mouse to drag it in any direction. Zoom in and out using the controls at the lower right of the screen or your mouse wheel. Click the ‘Reset’ icon to return to the default view.

You can navigate to the previous or next path in the list by using the arrows in the control at the upper right of the screen. The order of the pathways is determined by the sorting order and filters used in path view before expanded path view was opened. See the “Expanded Path View” section for more details.

>> Path View

You can collapse any set or pathway to facilitate comparison between your preferred ones. Click on the header of a set or a pathway to collapse it. An arrow at the right of the header indicates if the set or pathway is collapsed or expanded. Click again on a collapse set or pathway to expand it. 

Path View Settings

In the Settings panel, you can enable the set score to be displayed next to the number of steps for each set. 

Set scores are calculated by scoring functions governed by the criteria selected to run the analysis. Scoring functions assign penalties for undesirable elements in pathways. Therefore, lower scores are more desirable. The set score represents the added path scores for all pathways in the set.

Shared Path Library Preferences

There are a few options allowing you to customize how you see your results for Shared Path Libraries.

Pathway Options

Click on the Pathway Options icon to open a menu that allows you to select how much information you want to see displayed in your pathway. 

Pathway Actions

You can find a series of pathway actions on the right side of each pathway header.

Favorite pathway
Click the ‘Favorite’ icon to save this pathway as a favorite. 

Download pathway
To export a pathway, open the three-dot menu, select Download, and choose your preferred format from the menu.

• Report (PDF): Generates a PDF report including the analysis parameters, the pathway node scheme, and a description of each reaction (reaction scheme, protection requirements, typical conditions, and illustrative references).
• Image (SVG): Saves an image of the pathway as it is displayed in Pathway View.
• Reactions (RDF): Generates a Reaction Data File (RDF), which saves reactions in mol file format with all associated data.

Add to Shopping List
Open the three-dot menu and select ‘Add to shopping List’ to add the commercial compounds in the pathway to your shopping list.

Note: See “Shopping List” in the Analyses Dashboard User Guide to learn how to set up and use your Shopping List for selecting commercial compounds you would like to buy. You can then either export your list as a csv file, or directly to your Sigma-Aldrich® catalog e-commerce account. 

>> Shopping List