This section of the NovaDock Report represents the top ten ligand-receptor docking models predicted by NovaDock. To view or hide this section of the report, click on the expand arrow (small blue triangle) in its header.
The thumbnail preview image acts as an overview, with colored “heat bubble” spheres representing the centers of mass for ligand contacts. Each sphere represents the position of the ligand for one of the models listed in the corresponding table. Green is used to denote the lowest energy position (best) and red, the highest. Sphere size is proportional to cluster size, with larger being better.
The thumbnail preview is interactive and can be controlled with the mouse. To spin the model around its axis manually, slide the mouse laterally while holding down the left mouse button. To zoom in/out, use the mouse’s scroll wheel.
On the right, use the Filtering Method drop-down menu to specify whether or not to use funnel filtering, an energy based analysis method:
- Remove if not in binding funnel – Applies funnel filtering to models in the table, thereby eliminating models that do not land in an “energy funnel.”
- No filtering – Does not apply funnel filtering.
The Model Overview table contains sortable columns. Click once on a column header to make it active. Then click on the black triangle in the column header to sort the column numerically. Click on the triangle a second time to sort in the opposite direction.
The table below describes the columns in the Model Overview table.
| Column | Description |
|---|---|
| Model | The Model ID number. Models are ranked on a scale of 1 to 10 based on their Energy scores (see below). Use the checkboxes to the left of the Model ID column to specify which model(s) you would like to open when using the Open checked in new document link. |
| Energy | The energy score for each model. Lower (i.e., a larger negative number) is better. |
| Cluster size | During the simulations performed by NovaDock, thousands of plausible docking models are recorded. These models are clustered and one representative from each cluster is selected as the scaffold that is used to create the final prediction(s). Cluster size is the number of conformations in the cluster. A larger Cluster size is indicative of a lower-energy conformation. The lowest-energy conformations are associated with biologically-relevant structures. Therefore, with regard to determining ranking, a higher Cluster size is better. |
| Residue Contacts | The number of ligand residues in contact with receptor residues in a particular model. |
| Contacts Fulfilled | If a particular ligand or receptor residue was proposed when the NovaDock prediction was initiated, this column shows if it was included in the interface. |
To open one or more models as new Protean 3D documents – Leave checkmarks only next to the models you wish to open. Then click the link Open checked in new document.
To export the thumbnail preview image – Click the link Export model overview image. You may choose to save the image in .png, .gif, .jpg or .tiff formats.
Below this section of the NovaDock Report are sections for each individual model.
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