Rapid Binding Site Similarity Search Panel (Beta)
Search for receptors with binding sites similar to the specified structure.
To display this panel- click the Tasks button and browse to Other Applications → Rapid Binding Site Search (Beta)
- Using
- Features
- Additional Resources
Using the Rapid Binding Site Similarity Search Panel
The Rapid Binding Site Similarity Search panel searches a database of receptor structures for binding sites that resemble a query binding site, and returns the matching receptors aligned to your query. You can define the query in two ways: from a receptor and ligand in the Workspace, or from a model saved by a previous search. Use the Start with options to choose the input mode; the Inputs section changes to match your choice.
Before you begin, set the Database in the Settings section to the location of the search database. This location is remembered between sessions.
Searching from Structures in the Workspace
Select Structures in Workspace.
Define the ligand that marks the binding site. Select the ligand atoms in the Workspace and click Get from Selection, or select Pick and pick the ligand in the Workspace.
Adjust the search parameters in the Settings section as needed. For example, set the Similarity threshold that a hit must meet, the Maximum # structures to return, and any Filters that a receptor must satisfy.
Start the job.
Display the receptor in the Workspace, then click Load from Workspace next to Receptor. The receptor must contain a protein or nucleic acid structure.
Searching from a Previous Model (MIFs)
A search stores a model of the query binding site, described by its molecular interaction fields (MIFs). You can reuse a model produced by a previous search to run another search without reloading the original structures.
Select Model from previous search (MIFs).
Choose a previously used model from the Select or locate the previously used model option menu, or click Browse to locate a model file.
Adjust the search parameters in the Settings section as needed.
Start the job.
When the job finishes, the matching receptors are added to the project, aligned to your query binding site, together with a .csv file that lists the hits and their properties.
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.
Rapid Binding Site Similarity Search Panel Features
- Start with option
- Inputs section (Structures in Workspace)
- Inputs section (Model from previous search)
- Settings section
- Job toolbar
- Status bar
- Start with option
Select whether to start the search from structures in the Workspace or from a model created by a previous search. The Inputs section changes according to this choice.
- Inputs section (Structures in Workspace)
Specify the input structures. This section is present when Structures in Workspace is selected.
- Receptor load button
Specify the receptor to search with. Click Load from Workspace to use the current Workspace structure.
- Ligand selection tools
Specify the ligand that defines the binding site. Click Get from Selection to use the current atom selection, or select Pick to pick the ligand in the Workspace.
- Inputs section (Model from previous search)
Specify the input model. This section is present when Model from previous search (MIFs) is selected.
- Settings section
Set the database and search parameters. These settings are shared by both input modes, and are organized into Search settings (the database, similarity threshold, and GPU option) and Outputs settings (the number of structures returned, duplicate handling, and filters).
NOTE: The database must be accessible from the computer running the job.- Load from File link
Click this link to load search settings from a file.
- Database file path and Browse button
Specify the database to search. Click Browse to locate the database.
- Similarity threshold text box
Specify the minimum similarity, on a 0 to 1 scale, for a result to be included.
- Use GPU option
Select this option to run the search on a GPU host.
- Maximum # structures text box
Specify the maximum number of structures to return.
- Drop duplicates option and option menu
Select this option to remove duplicate results, then choose the property used to identify duplicates from the based on option menu: PDB ID, UniProt ID, PFam, Protein Name, or Gene Name.
- Filters button
Click Filters to open a pop-up in which you define rules that a receptor must satisfy to be included in the results.
- Filtering rules
Select the check box for each rule you want to apply, and specify the value to match. Available rules are Ligand, UniProt ID, Family, PFam, Organism, Taxonomic Lineage, and Protein Name. The Ligand rule uses Required or Excluded rather than a value.
- Filter button
Click to add a filtering rule.
- Check All and Clear All links
Click Check All to select all rules, or Clear All to clear all rules.
- Job toolbar
Manage job submission and settings. See Job Toolbar for a description of this toolbar.
The Job Settings button opens the Rapid Binding Site Similarity Search (Beta) - Job Settings Dialog Box, where you can make settings for running the job.
- Status bar
to reset the panel to its default settings and clear any data from the panel.If you can submit a job from the panel, the status bar displays information about the current job settings and status for the panel. The settings include the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.
The status bar also contains the Help button
, which opens an option menu with choices to open the help topic for the panel (Documentation), launch Maestro Assistant, or if available, choose from an option menu of Tutorials. If the panel is used by one or more tutorials, hover over the Tutorials option to display a list of tutorials. Choosing a tutorial opens the tutorial topic.