Template Ligand Finder (Beta)

Template Ligand Finder panel is for ligand-binding mode prediction and cryptic binding site identification. Rapidly identify and visualize homologous proteins based on both protein and ligand similarity to uncover potential template ligands as references for IFD-MD.

To open this panel, click the Tasks button and browse to Receptor-Based Virtual Screening → Template Ligand Finder. Alternatively, click the Tasks button and browse to Induced Fit Docking → Template Ligand Finder.

  • Features
  • Additional Resources

Template Ligand Finder Features

Input Settings

Set protein and the optional ligand to search for template ligands.

Protein and chain selection menus

Select the source (Project Table, from File, or from an entry in the Workspace) for the desired protein from the dropdown menu and click the Load button. Select the chain letter from the adjacent dropdown menu (this is required if the protein is from the Workspace). Click the Pick button to make the selection for the chain in the Maestro workspace.

Ligand and name selection menus

Select the source (Project Table, from File, or from an entry in the Workspace) for the optional ligand from the dropdown menu and click the Load button. Also select the ligand name from the adjacent dropdown menu. Click the Pick button to make the selection for the ligand in the Maestro workspace.

Search Filters

Max # results to return option

Enter a value in the text box to set the maximum number of results to return in the Search Results.

Min sequence ID (%) option

Enter a value in the text box to set the threshold for querying BLAST hits. Hits with a sequence identity value below the threshold will be ignored. The default value is 25.

Advanced options menu

Clicking the blue text opens a menu with several settings for Structure Options, BLAST Search Options, and ID Filters.

Structure options
Use the text boxes, arrow keys and dropdown menu to adjust the Minimum Tanimoto score, Maximum resolution (in Å), and Release date range.
BLAST Search options
Use the text boxes and arrow keys to adjust the Minimum similarity (%), E-value, and the Maximum # of hits to analyze.
ID Filters options
Click the blue Add Filters link to add Uniprot or Taxonomy filters.

 

Search Results

Search Results Table

The search results are displayed in the table, and can be sorted by value by clicking the chevron icon that appears when hovering over a column header.

Export Table link
Click the link to export the contents of the table as a CSV file.
Import complexes link
You can import complexes on to their respective Workspaces by selecting rows from the table and then clicking the link. Multiple rows can be selected by pressing Shift or Cmd while making a selection.

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