Template Ligand Finder Panel

Find template ligands for IFD-MD by identifying homologous protein-ligand complexes based on sequence and ligand similarity.

To open this panel, do one of the following:

  • Click the Tasks button and browse to Receptor-Based Virtual Screening → Template Ligand Finder
  • Click the Tasks button and browse to Induced Fit Docking → Template Ligand Finder
  • Using
  • Features
  • Additional Resources

Using the Template Ligand Finder Panel

Use this panel to search for homologous protein-ligand complexes that can serve as template ligands for IFD-MD Panel. The search runs BLAST to identify proteins with sequence similarity to the target, aligns matching structures, and optionally scores ligand similarity using Tanimoto coefficients. The results can also reveal potential cryptic binding sites by identifying ligand-bound conformations in homologous proteins.

To search for template ligands:

  1. Load a prepared protein structure using the Protein option menu and click Load. Select the target chain from the Chain option menu, or click Pick to select the chain in the Workspace.

  2. Optionally, load a ligand using the Ligand option menu. Providing a ligand enables Tanimoto similarity scoring, which helps identify homologous complexes with similarly shaped ligands.

  3. Adjust Max # results to return and Min sequence ID (%) if needed. Click Advanced options to configure additional filters for structure resolution, BLAST search parameters, and Uniprot or Taxonomy ID filters.

  4. Click Run Search. The search typically completes in 30 to 60 seconds.

  5. Review the results in the Search Results table, which reports sequence identity, sequence similarity, resolution, Tanimoto score, and RMSD for each hit. Select rows and click Import Complexes to load the protein-ligand complexes into the Workspace. The imported complexes are aligned to the target protein, making it straightforward to compare binding sites and evaluate candidate template ligands.

To write out the input file and a script for running the job from the command line, click the arrow next to the Settings button and choose Write. For information on command usage and options, see template_ligand_search.py Command Help.

Template Ligand Finder Panel Features

Protein option menu

Choose the structure source for the protein structure.

  • Project Table (selected entries)—Use the entries that are currently selected in the Project Table.
  • Workspace (included entry)—Use the entry that is currently included in the Workspace. Only one entry must be included in the Workspace. When this option is selected, a Load button is displayed to the right.
  • File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed. The allowed file types are: Maestro and PDB.
Chain option menu

Select the chain to analyze from this option menu, which is populated from the loaded protein structure. Click Pick to select a chain in the Workspace instead. Only available when a protein is loaded.

Ligand option menu

Choose the structure source for the optional ligand. Providing a ligand enables Tanimoto similarity scoring in the results.

  • Project Table (selected entries)—Use the entries that are currently selected in the Project Table.
  • Project Table (n selected entries)—Use the entries that are currently selected in the Project Table or Entry List. The number of entries selected is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and select entries. When this option is selected, a Load button is displayed to the right.
  • Project Table (selected entry)—Use the entry that is currently selected in the Project Table. Only one entry must be selected.
  • Workspace (included entries)—Use the entries that are currently included in the Workspace, treated as separate structures.
  • Workspace (n included entries)—Use the entries that are currently included in the Workspace, treated as separate structures. The number of entries in the Workspace is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and include or exclude entries. When this option is selected, a Load button is displayed to the right.
  • Workspace—Use the contents of the Workspace as a single structure.
  • Workspace (included entry)—Use the entry that is currently included in the Workspace. Only one entry must be included in the Workspace. When this option is selected, a Load button is displayed to the right.
  • File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed. The allowed file types are: Maestro.
  • Files—Use structures from the specified files. When this option is selected, the File name text box and Browse button are displayed. The allowed file types are: Maestro.
  • Phase Database—Use the structures in the specified Phase database. When this option is selected, the File name text box and Browse button are displayed. Click Browse and navigate to the database you want to use. The database name is displayed in the text box when you click Open in the file selector. You can also enter the database name in the text box. You will need to do this if the database is not available on the file system, and also select Remote database.
  • Phase Database (local)—Use the structures in the specified local Phase database. When this option is selected, the Local database text box and Browse button are displayed.
  • Phase Database (remote)—Use the structures in the specified remote Phase database. When this option is selected, the Remote database path text box is displayed. Enter the full path to the database on the remote host in the text box.
  • Database—Use the structure whose identity is recorded in the specified SQL database. When this option is selected, the File name text box and Browse button are displayed, so you can specify the database.
Name option menu

Select the ligand name from this option menu, which is populated from the ligands detected in the loaded structure. Click Pick to select a ligand atom in the Workspace instead. Only available when a ligand is loaded.

Max # results to return text box

Specify the maximum number of results to return in the search results. The default is 20.

Min sequence ID (%) text box

Specify the minimum sequence identity threshold for BLAST hits. Hits with a sequence identity below this threshold are excluded. The default is 25.

Advanced options link

Click this link to open a popup with settings for structure options, BLAST search options, and ID filters.

Structure Options section

Settings for filtering search results by structural properties.

Min Tanimoto score text box

Specify the minimum Tanimoto similarity score for ligand filtering. The range is 0.0 to 1.0, in increments of 0.05. The default is 0.0. Only available when a ligand is specified.

Max resolution (Å) text box

Specify the maximum crystallographic resolution in angstroms. Structures with resolution above this value are excluded. The default is 4.5.

Release date range

Use the Start and End date pickers to restrict results to structures released within the specified date range.

BLAST Search Options section

Settings for the BLAST homology search.

Min similarity (%) text box

Specify the minimum sequence similarity percentage for BLAST hits. The range is 0 to 100. The default is 0.

E-value text box

Specify the E-value threshold for BLAST hits. The range is 0.01 to 10.0. The default is 1.0.

Max # hits to analyze text box

Specify the maximum number of BLAST hits to analyze. The range is 1 to 500. The default is 500.

ID Filters section

Filter search results by Uniprot or Taxonomy IDs.

Add Filter link menu

Click this link menu to add an ID filter. Choose Uniprot or Taxonomy to add a filter row. Each filter row has an inclusion mode (Include or Exclude), a text field for entering comma-separated IDs or a file path, and a browse button. Up to 8 filters can be added.

Run Search button

Click this button to run the template ligand search with the current settings.

Search Results section

Displays the results of the template ligand search.

Search results table

The search results are displayed in the table. Sort by column by clicking the arrow icon that appears when hovering over a column header. Columns include Rank, PDB ID, E-value, Seq ID %, Seq Sim %, Uniprot ID, Taxonomy ID, Resolution, Tanimoto, and RMSD. The RMSD is calculated by aligning the C-alpha atoms of the input protein with those of each homologous structure, based on a pairwise sequence alignment.

Export Table link

Click this link to export the contents of the table as a .csv file.

Import Complexes link

Select rows in the table and click this link to import the selected complexes into the Workspace. Select multiple rows with shift-click and control-click.

Reset button

Reset the panel to its default settings.

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