Pocket Detection
Identify small-molecule binding pockets on protein surfaces.
Menu: Proteins → Detect Pockets
Guided tour: Launch in MolModa
This plugin also calculates pocket properties using the fpocket algorithm (FPocketWeb).
Where to find it
Dialog
Parameters
| Parameter | Default | Description |
|---|---|---|
makemolinputparams |
— | — |
| Provide pocket-filling pseudo atoms for visualization | No | — |
Optional Pocket Detection Parameters
Unless you are an expert user, these advanced parameters are best left unmodified
| Parameter | Default | Description |
|---|---|---|
| Minimum radius of an alpha-sphere | 3.4 |
— |
| Maximum radius of an alpha-sphere | 6.2 |
— |
| Distance threshold for clustering algorithm | 2.4 |
— |
| Clustering method for grouping voronoi vertices | s |
— |
| Distance measure for clustering | e |
— |
| Minimum number of a-sphere per pocket | 15 |
— |
| Minimum proportion of apolar sphere in a pocket (remove otherwise) | UserArgType.Text |
— |
| Minimum number of apolar neighbor for an a-sphere to be considered as apolar | UserArgType.Color |
— |
| Number of Monte-Carlo iterations for calculating each pocket volume | 300 |
— |