Below the Model Overview section of the NovaDock Report are expandable sections for each of the individual models (e.g., Model 1, Model 2, etc.). To view or hide this section of the report, click on the expand arrow (small blue triangle) in its header.
The image in each Model shows the predicted ligand-receptor docking model. The receptor and ligand chains are represented by green and yellow ribbons, respectively. Interface residues are rendered in “ball and stick” format, and can be seen more clearly by zooming in on the image, as described in the table below.
The thumbnail preview is interactive and can be controlled with the mouse:
|To spin the model manually||Slide the mouse laterally while holding down the left mouse button.|
|To zoom in/out||Use the mouse’s scroll wheel.|
|To view the location of a particular residue||Select the residue in the table on the right by clicking on its row. The residue will be highlighted in light blue in the image.|
|To view the location of the receptor and ligand chains||To the right of the image, click the links next to Receptor chain or Ligand chain. The associated chain will be highlighted in light blue.|
Information about the model appears to the right of the thumbnail preview.
|Molecule||Model ID number.|
|Energy||The energy score for each model. Lower 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.|
|Cluster Energy||The average energy for the clusters in the model.|
|Residue Contacts||The number of ligand residues in contact with receptor residues in a particular model.|
|Receptor chain||A link that can be pressed to select the receptor chain (green ribbon) in the thumbnail preview image. The associated chain will be highlighted in light blue.|
|Ligand chain||A link that can be pressed to select the ligand chain (yellow ribbon) in the thumbnail preview image. The associated chain will be highlighted in light blue.|
Additional information about the model appears in the Model table. Selections made in this table are simultaneously selected in the thumbnail preview.
|Residue||A label for each interface residue. It consists of the chain where the residue is located, its amino acid abbreviation and the residue number (e.g., A:HIS 131).|
|Molecule||The molecule to which the interface residue belongs (i.e., Receptor or Ligand).|
|Intermolecular Contacts||A list of contacts between the two binding partners.|
|Proposed||If a particular ligand residue was proposed when the NovaDock prediction was initiated, this column shows if that residue was included in the interface.|
Each Model section also includes a separate area called Models in Cluster.
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