The Activity Miner component for Forge and Torch enables the rapid navigation of complex SAR, highlighting key activity changes. Critically, Activity Miner gives you a clear rationale for changes in activity and provides inspiration for how to exploit this knowledge in future design iterations.
Activity Miner enables you to:
- Rapidly navigate structure activity relationships, even on large datasets
- Find the critical regions of activity using matched molecular pairs and activity cliff analysis
- Understand the electrostatic and shape changes that cause a difference in activity and selectivity
- See how new compounds relate to the entire history of the project, finding relationships that would otherwise be missed
- Design new compounds with confidence, based on the insights you gained in Activity Miner.
Activity Miner uses the concept of ‘disparity’ or ‘activity cliffs’ to highlight regions in your SAR where major changes have been observed. The disparity of a pair of molecules is calculated by dividing the activity difference of the pair by the distance between them.
Multiple views of your SAR mean maximum insight
Activity Miner is focused on explaining the reasons behind an activity change. It offers multiple views of the data to help you find key molecule pairs in your SAR. For each pair, Activity Miner shows you how the electrostatic and shape properties differ, building an understanding of how to design better compounds with better properties.
The different views enable you to focus on different aspects of your SAR.
See all your data
The Disparity Matrix is a sortable table of all molecule pairs, showing how each compound compares with all other compounds.
- Strong colors correspond to large disparities, making it easy to identify a drop off or increase in potency
- Select a cell to display a pair of compounds in the 3D window, where you can explore similarities and differences in the electrostatics and shape
- Expand the matrix with multiple activities to highlight key selectivity information
- Filter and sort the matrix to find the most similar molecule pairs.
Explore the SAR around one compound
The innovative Activity View combines near neighbor analysis with activity cliff data, showing the local SAR colored by activity change.
- Choose a compound of interest and compare it with its close neighbors, viewing activity, selectivity, similarity and differences
- Structural differences are highlighted in the view, making it easy for you to see what changes you’ve already made
- Select any of the neighbors to inspect the electrostatic and shape differences in more detail in the 3D window
- Double click on a neighbor to make it the new focus molecule and compare it with its nearest neighbors.
Find the most significant changes
The top pairs table highlights critical points in your SAR. It displays pairs of molecules that show the greatest change in activity relative to the change in structure, enabling you to understand the changes that have the most impact on your project.
The table enables you to:
- Find important pairs of molecules with the structural changes highlighted
- See key changes in activity and physicochemical properties for each pair
- Save pairs as favorites for further analysis
- Understand the electrostatic and shape differences in 3D for every change
- Re-sort the table by any property or value.
Gather similar compounds together
The Cluster View (available in Forge only) makes it easy to see how your compounds relate to each other using cluster analysis based on 3D or 2D similarity.
- Get an insight into the chemical diversity of your dataset
- Visualize the spread of activities across clusters to identify homogenous subsets and important outliers
- Tag or export molecules according to cluster membership
- Display any cluster in Forge for further analysis
- Select any compound to display the activity and structure in 2D and 3D.