ligand, conservation, distance, export

Analyze Binding Sites Panel

Calculate sequence conservation in multiple alignment columns that are within a certain spatial distance from ligand residues, and filter the alignment sequences based on the sequence conservation.

To open this panel, click the Other Tasks button on the toolbar and choose Analyze Binding Sites.

  • Using
  • Features
  • Additional Resources

Using the Analyze Binding Sites Panel

To analyze a binding site, you must have a sequence and a structure for the reference, and the structure must have at least one ligand (it can have more). Next, you must have a set of sequences that are aligned to the reference, which you can obtain from a BLAST search (Homologs button on the toolbar) followed by an alignment (Align button on the toolbar or Align menu). If you want to do the analysis for sequences other than the reference, you must have structures with ligands for those sequences.

When you open the dialog box, the reference sequence is analyzed and annotated with ligand contacts (for all ligands), and the columns for the residues that are in contact with the ligand (or first ligand) are selected. Sequences that have more than 85% identity with the reference residues that are in contact with the ligand (or the first ligand) are also selected by default.

You can change the sequence and select the ligand with the Ligand option menus. When you change the sequence, the new sequence is analyzed and annotated and the column selection updated for the new ligand. Changing the ligand updates the column selection.

The Distance analysis is useful for examining the average conservation within a set of sequences. The analysis could be repeated for different queries to obtain a comparison of the average conservation for the queries.

Analyze Binding Sites Panel Features

Ligand option menus

Choose the sequence and ligand for the sequence from these option menus, if the structure for the sequence has more than one ligand. The column selection changes to represent contact with the chosen ligand. The analysis is done on the basis of the chosen sequence and ligand.

Conservation section

In this section you can select sequences based on the degree of conservation of residues in the active site (i.e. residues that are in contact with the ligand).

Conservation threshold slider

Use this slider to adjust the percentage sequence conservation for selecting sequences in the Multiple Sequence Viewer/Editor Panel. As you change the value, the selection is updated to reflect the new threshold. The default is 85%. The slider is synchronized with the text box below.

Select Sequences with option menu and text box

Select sequences that match the condition chosen from the option menu and the threshold set in the text box. The conditions allow you to select sequences that are similar to or different from the reference, within a threshold. The text box and the slider are synchronized.

Distance section

In this section you can analyze the average identity, similarity, and conservation of the residues in the alignment to the reference residues that are within a range of distances from the ligand. This allows you to assess how these quantities change as the binding site is made smaller or larger.

Scan from N to M angstroms boxes

Specify the range of distances over which the analysis is performed. The increment is 1 Å. The distance is the value used for binding site detection: residues with any heavy atom within the specified distance of a ligand heavy atom are identified as binding-site residues.

Calculate button

Calculate the average identity, similarity, and conservation in the binding site over all sequences, for the range of distance thresholds that define the binding site.

Distance table

This table reports the results of the analysis. Each row gives results for a particular distance, reporting the identity, similarity and conservation values for the binding site residues defined by the distance, averaged over all sequences in the alignment.

Export link

Export the table data to a CSV file. Opens a file selector, in which you can navigate to a location and name the file.

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