Find binding sites that resemble one of your structure's pockets, for example to find new chemical matter or possible off-targets.
Prerequisites: the structure is open in the Workspace.
- In the Collections panel, open the ⋮ menu of the structure and select Find similar pocket. The Pocket Similarity Search panel opens on the left.
- Under Detected pocket, select the pocket. Its residues are listed and highlighted in the 3D viewer.
- Check the settings. The defaults suit most searches: Match score threshold 0.2, Pockets with ligands only on, up to 500 results.
- Optionally, open a filter, for example Filter by species, and add values.
- Click Search.
Result: a collection tagged Pocket Search appears in the Collections panel. Hits are added as they are found and sorted by score. Click the eye icon of a hit to see it superposed on your pocket.
- Search with a subpocket: in step 2, choose Custom residues and enter at least 3 residues, for example
A:93, A:96, A:138, or click them in the 3D viewer.
- Look for off-targets: turn off Pockets with ligands only, so that empty pockets are searched too.
- Compare across proteins: turn on Best match per protein only.
- Test quickly: use Filter by structure with a few structure codes. The search then takes seconds.
- Check what you searched for: in the collection's ⋮ menu, select See query details.
- Start from the pocket table: open Show Pockets, then select Find similar pocket in a row's ⋯ menu.
- The search shows Queued: 3 searches are already running. Yours starts automatically when one finishes.
- The search takes very long: a search over the whole database can take hours. Add filters, or lower Maximum number of results. You can look at the hits found so far.