Cerius²·Ludi

6.5       Tutorial lesson 5: Ludi library management

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The Ludi library management commands allow you to create and add to fragment libraries for Ludi.

In this tutorial you will add a new entry to a Ludi library and then use that library in a search for fragments that can bind to trypsin.

This tutorial takes about 15 minutes to complete and covers:

• Setting Ludi to run from a local Ludi library.

• Adding an entry to a local Ludi library.

• Using library filters.

To start the tutorial select the File/Load Model... command, set File Format to MSI, go to the Cerius2-Resources/LUDI directory and double click fragment.msi.

The molecule displayed on the screen is o,m-diamino-toluene. This is the molecule you will be adding to a Ludi library. Its Cerius² object name is fragment.

Type the following commands in the textport: !cp ./Cerius2-Resources/LUDI/tut5_usr_lib_std.str user_lib.str !cp./Cerius2-Resources/LUDI/tut5_usr_lib_std.trg user_lib.trg

This will add the following files to your current directory:

user_lib.str 


user_lib.trg

The Ludi deck of cards will appear containing the ACTIVE SITE VIEWER, LUDI LIBRARY, ANALOGS BASED DESIGN and RECEPTOR BASED DESIGN cards.

2.   Adding a new entry to the Ludi library

Go to the LUDI LIBRARY card and click Add Entry.

The Ludi Add Library Entry control panel will appear.

Each library comprises two files, a structure file, containing atomic coordinates, and a targets file, describing the interaction sites of the fragments.

There are two types of libraries, a standard library, used when Ludi is run in standard (de novo) mode, and a link library, used when Ludi is run in link mode.

Ludi libraries may be either PDB_TEXT, MOL_TEXT or MOL_BINARY format. A library may not mix formats. When you create a New Library, you must specify which format to use. When you add to an existing library, Ludi figures out the format of the library and adds the appropriate entry.

In this case, you are going to be adding the current molecule to the existing library user_lib.str.

On the Ludi Add Library Entry control panel, make sure that the Add button is set to Existing Library. Using the file browser, locate the copy of user_lib.str in your home directory. Click SELECT to initialize the Library Name field.

Since you are creating an entry for a standard library and not for the link library leave Link Entry unchecked.

Enter FR1 for the Label and click the ADD Current Model to Existing Library button.

The label FR1 identifies the molecule in the library. It must be a 3 character string and it must be unique against all existing labels in the library. An error message will be issued if the string is not unique and the library will not be corrupted.

3.   Add Library reports in the textport

When the job has completed and the fragment has been added to the library, the text port will report that three entries were added to the library for the molecule fragment. This is because there are more than one set of possible target sites for this molecule.

Now that the molecule has been added to the library it can be deleted from Cerius².

Select the fragment by clicking just to the left of its ID number in the Visualizer Models panel. Click the minus sign above the model list on the Visualizer to delete the fragment and click OK when prompted.

4.   Specifying the local Ludi library

Go to the LUDI LIBRARY card and click Library Spec.

The Ludi Library Specification panel will appear.

Note that the Ludi Library Specification panel is divided into two sub-panels, one for each of the two types of Ludi libraries: the De Novo Library which is used when Ludi is run in standard (de novo) mode and the Link Library which is used when Ludi is run in link mode.

In this tutorial you will use the de novo library designed you just modified.

Set the Library Type under De Novo Library to User. Using the file browser, locate the copy of user_lib.str and click SELECT.

5.   Loading the trypsin-benzamidine system

Now you will use the new library to find potential ligands for trypsin. First, load in the trypsin-benzamidine system.

To load the trypsin-benzamidine system, select the File/Load Model... command, set File Format to MSI, go to the Cerius2-Resources/LUDI directory and double click first benzamidine.msi and then trypsin.msi.

6.   Searching the modified fragment library

You are now ready to search the modified library for ligands that fit the trypsin cavity.

On the RECEPTOR BASED DESIGN card, click Find Hits.

The Ludi Receptor Based Design panel will appear.

Click the Defined Current Model as Receptor button to initialize trypsin as the receptor

Leave Search Sphere Radius set to 5.00 Angstroms.

This indicates that only trypsin atoms within 5 Å of the Search Sphere Center Coordinates are to be used in fitting fragments from the specified fragment library.

Fill Search Sphere Center Coordinates with the coordinates of the C1 atom in benzamidine. This is the only phenyl carbon without a hydrogen. To do this, make sure benzamidine is the current model by clicking its (diamond-shaped) currency button in the Visualizer. Then turn off trypsin's (square) visibility button. Benzamidine should now appear alone on the screen. If necessary, press the right mouse button to rotate benzamidine into view and the two rightmost mouse buttons to zoom in on the molecule. Next, click the C1 atom of benzamidine. To make sure you have selected the correct atom, look at the report in the textport. It should read: Model(name=benzamidine):Chain(name=ABEN):Residue(type=BEN 1):Atom(name=C1) Now click Define Center From Selected Atoms.

When you are designing inhibitors de novo, you may wish to fill in the Search Sphere Center Coordinates parameter by picking an atom that is part of the active site of the protein. Or, you could create a small molecule (e.g., with a command like Build/3D-Sketcher...) and place it in the active site.

You can then pick atoms in the small molecule to fill in the Search Sphere Center Coordinates by clicking the Define Center From Selected Atoms button. The small molecule can be positioned wherever you like in the active site. As long as Link Sites is checked, Ludi ignores all molecules except the receptor so the small molecule's presence does not perturb Ludi.

To begin the Ludi calculation, click the Find Ludi hits on the Ludi Receptor Based Design panel.

Open the Job Control panel by clicking Job Control menu item on the RECEPTOR BASED DESIGN card. Click the Update button and then click Monitor Logfile.

This will open an xterm window displaying the log file. At the end of the run, the logfile will report that six hits were found. If you get an error message that says the logfile does not exist, you've clicked the Monitor Logfile button too soon. Wait a few moments and try again.

7.   Loading the results of the Ludi run

Proceed with this step only after the log file shows that the run is complete.

Click Load on the RECEPTOR BASED DESIGN card. When the Ludi Load panel appears, find the .run file for the run name noted on the Ludi Job Control control panel (you may have to hit the update button to see the most recent job) and click SELECT. Load the hits into the Ludi Score Table by clicking the Load button (make sure that the Hits parameter is toggled on). Note that you have the option (unchecked by default) of loading the results into a QSAR study table. This tutorial will assume that you are viewing the results in the default Ludi Score Table and not the study table.

The Ludi Score Table will appear listing the six hits.

If all the scoring information is available (This is true if the run was not killed and if you have not deleted files from the run directory.) the fragments are loaded in by score from highest to lowest. If the scoring information is not available, the fragments are loaded in the order in which they were found in the Ludi library.

8.   Filtering Ludi libraries

You may also filter Ludi libraries using the Library_Filters options on the LUDI LIBRARY card. These options allow you to require or reject specified functional groups in the Ludi hits.

Now you will repeat the last Ludi run using a library filter.

Select Library Filters De Novo Library from the Ludi Library menu. When the Ludi de Novo Library Filters control panel appears, set the De Novo Library Filter Lists to Required_Group, enter HNH in the text field and set the list operation parameter (looks like a minus sign) to Add.

9.   Searching the filtered library

Repeat the Ludi run by clicking the Find Ludi Hits. Monitor the logfile for job completion.

When the Ludi job has finished the logfile should report that it has found five hits.

10.   Loading the results of the filtered run

Before loading the results of this Ludi run, delete the hits from the previous run.

Select the first model by clicking just to the left of its ID number in the Visualizer Models panel. Add subsequent models to the selection by holding down the shift key and clicking to the left of their ID numbers. The following models should now be selected: G61 fragment G35 H72 TRP X16 Click the minus sign above the model list on the Visualizer to delete the fragment and click OK when prompted.

Use Load on the RECEPTOR BASED DESIGN card as above.

11.   Reviewing the results of the filtered run

Note that the compound TRP that was found in the first run is not present in the second run because it does not contain the HNH group.

Now clear the filter list.

Select Library Filters De Novo Library from the Ludi Library menu. When the Ludi de Novo Library Filters control panel appears, set the De Novo Library Filter Lists to Required_Group and click Clear Selected Filter to clear the required group filter list.

12.   Filtering the Library with a Rejected_Group List

You may also specify groups which are to be rejected during a Ludi run.

Select Library Filters De Novo Library from the Ludi Library menu. When the Ludi de Novo Library Filters control panel appears, set the De Novo Library Filter Lists to Rejected_Group, enter HNH in the text field and set the list operation parameter (looks like a minus sign) to Add.

13.   Searching the filtered library

Repeat the Ludi run by clicking Find Ludi hits and monitoring the logfile for job completion.

When the Ludi job has finished the logfile should report that it has found one hit.

14.   Loading the Results of the Filtered Run

Before loading the results of this Ludi run, delete the hits from the previous run.

Select the first model by clicking just to the left of its ID number in the Visualizer Models panel. Add subsequent models to the selection by holding down the shift key and clicking to the left of their ID numbers. The following models should now be selected: G61 fragment G35 H72 X16 Click the minus sign above the model list on the Visualizer to delete the fragment and click OK when prompted.

Use Load on the RECEPTOR BASED DESIGN card as above.

15.   Reviewing the results of the filtered run

The compound TRP was the only hit found this time. It is the only hit that did not contain the HNH group.

16.   Tutorial complete

In summary, you have used the Ludi library management tools to add a new entry to a Ludi library, to specify a non-default library to be used in a Ludi run and to filter the library based upon a required or rejected functional group.

To assure a fresh start for the next tutorial, reinitialize Cerius2. Select File/New Session... and click Confirm on the prompt that appears.

This has the effect of deleting all objects from the Model Window and reinitializing all of the parameters in Ludi.

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