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Virtual Screening Workflow Panel |
The Virtual Screening Workflow panel enables you to set up and run jobs to screen ligands against one or more targets. The workflow includes ligand preparation, filtering, and up to three docking stages with Glide, progressing from HTVS to SP to XP docking. For docking to multiple targets (ensemble docking), you can specify docking score offsets for each target.
To open the Virtual Screening Workflow panel, you can:
Choose Applications → Glide → Virtual Screening Workflow. in the main window.
This panel can be used to run the entire sequence of jobs in the Virtual Screening Workflow. The panel sets up the input files for LigPrep, QikProp, and Glide ligand docking and submits them to the selected host in order.
When you run the workflow, you can pregenerate Glide grids for the desired receptors, or generate grids from the Workspace structure. For more information on generating Glide grids, see the Glide Receptor Grid Generation Panel topic.
The ligand files for the workflow can consist of 2D structures or 3D structures. If you supply 2D structures, you must run the ligand preparation part of the workflow to convert the structures to 3D for docking. This stage runs a LigPrep job, with the standard options for most parts of the LigPrep process. You can control some of these options, but if you want to use other options, you should run LigPrep on the ligands independently. For more information, see the LigPrep Panel topic, or the LigPrep User Manual. Because LigPrep does not sample conformations of 7-membered or larger rings, you can run a MacroModel job after LigPrep to sample these rings.
Prefiltering of the ligands can also be performed as part of the workflow. If
you want to use the Lipinski Rule option, you must run QikProp to obtain the
required properties. You can run QikProp as part of the workflow, regardless of
the ligand source. If you have already run QikProp, you do not need to run it
again. The reactive groups filter is a predefined filter that removes ligands
with these groups. If you want to specify a custom filter, you can provide an
input file for ligfilter, which will then filter the structures,
or set up the filter in a graphical interface. You can also choose whether to
filter the ligands before or after preparation. For more information
on ligfilter, see
Appendix D of the Maestro User Manual
The full workflow includes three docking stages. The first stage performs HTVS docking. The ligands that are retained are then passed to the next stage, which performs SP docking; the survivors of this stage are passed on to the third stage, which performs XP docking. At each stage you can decide how many ligands are kept, and whether the ionization and tautomeric states of each ligand are kept.
The stages of the job are managed by a master job, and the work can be divided into subjobs, which can in turn be distributed over multiple processors. The master job runs locally, but you can specify hosts to run the ligand preparation (LigPrep) and grid generation and docking (Glide) and the number of processors to use on each host, in the Job Settings dialog box. For docking you can specify the number of subjobs, in the Separate into N subjobs text box, or select Adjust to automatically adjust the number of subjobs so that each takes between 1 and 10 hours. For effective load balancing of a distributed job, the number of subjobs should be several times the number of processors.
The workflow is intended to be robust, so that if a subjob fails, the master job attempts to rerun the job a few times before quitting.
If you want to incorporate the results in to the Maestro project, you can choose Append new entries from the option menu in the Output section of the Job Settings dialog box.
You can dock the ligands to multiple receptors in the workflow, and provide
an offset for the GlideScore so that the results from different receptors can be
compared. If you want to merge more results later, you can do this with the
script $SCHRODINGER/utilities/glide_ensemble_merge. Use the
-h option for the syntax of this script.
The main part of the Virtual Screening Workflow panel consists of five tabs for setting up screening jobs. These tabs are described in separate topics.
The Job toolbar is used to make settings for a job and to start it.
Enter a name for the job in this text box.
This button opens the Job Settings dialog box. The arrow to the right opens a menu, from which you can make settings or perform actions that are related to the job.
The menu items are described below.
This icon indicates when there are jobs running for the application that belong to the current project. It starts spinning when the first job starts, and stops when there are no more jobs running. If a job fails to start, it changes to an exclamation point.
Clicking the button shows a small job status window that lists the job name and status for all active jobs submitted from the current panel (for Jaguar and MacroModel this means all jobs from any of the application panels). You can double-click on a row to open the Monitor panel and monitor the job, or click the Monitor button to open the Monitor panel and close the job status window. The job status is updated while the window is open. If a job finishes while the window is open, the job remains displayed but with the new status. The rows are colored according to the status: yellow for submitted, green for launched, running, or finished, red for incorporated, died, or killed. Click anywhere outside the window to close it.
Run the job with the current job settings.
The status bar displays information about the current job settings for the panel. This includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. It also displays a message for a short time when you start a new job.
The status bar also contains the Help button, which opens the help topic for the panel.
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