The following was done to create a sample dynamics file to operate on: The "active site" of the HIV-1 protease/inhibitor complex was created using sets under Build/Edit, Delete, Substructure. A sphere (6 A) was defined using as the center point(s) all of the "substructures" of the A74704 inhibitor. (Then you have to press invert to retain the selected atoms and delete the remainder.) Dynamics was run on this system where the HIV-1 "active site" was set as an aggregate and the A74704 inhibitor was free to move.

The other dynamics parameters were left in their SYBYL default configuration.

This particular example is fairly tricky, as we have have to convince SYBYL and HINT to accept the molecule definitions for the two interacting species. Since HINT requires two interacting species to be in separate Molecule Areas, we will read the complex in twice. From the File pulldown on the menubar select Read... and select hiv1_a74704_site.mol2 for M1. Repeat and put the same molecule in M2.

Now, use Analyze, Dynamics and Analyze Dynamics to bring up the history selection dialog. Select hiv1_a74704_site.his and choose M2 as the Molecular Area for the Spreadsheet. The next three dialogs concern which times in the dynamics run are to be placed in the spreadsheet. There are 1000 data points in the spreadsheet, we want to select the most interesting sample for HINT analysis. Try Data reduction Interval of 5, Data start of 0 and Data end of 499. This should create a table of 101 rows.

Making sure that none of the Table columns or rows are selected, press the Table AutoFill button, select Column and HINTSCORE from the New column type menu. This Add HintScore Columns dialog will calculate HintScores for three distinct situations: 1) InterMolecular [each Ligand (row)] is used when each row of the table is a different ligand binding to the same (rigid) receptor; 2) InterMolecular [with Prototype Conformer] is used when only one ligand is in teh table, but many conformations for that ligand are in the table; and 3) IntraMolecular [requires Prototype] is used for an intramolcular HINT analysis of a single molecule with multiple conformations. The latter two are appropriate for dynamics or other conformation expanded tables. Choice two, InterMolecular [with Prototype Conformer] is what we need for this tutorial.

We must select and partition both the "Receptor" and the "Prototype". First the Receptor (in fact you must always partition the Receptor first when using this option): Select the Atoms... in M1 using the Substructures... button in the Atom Expression dialog. Choose CBZ301 VAL302 CORE303 VAL304 CBZ305 H2O401 and press OK to the Substructures list. Now in Atom Expression dialog, press Invert to select everyting in M1 except the ligand substructures. Select OK in the Atom Expression dialog. Now in the Partition Molecule dialog, select Partition Method: Dictionary and Solvent Condition: Neutral. Press OK to Partition the Receptor. The LogP should be 1.80.

Now press the Partition Prototype... button. The prototype is a single conformation of the ligand molecule that matches in all respects except coordinates the conformations in the Table. In this case to get the Prototype, choose the Atoms as above, but this time use M2, and do not press the Invert button. Use Partition Method: Calculate and press OK to the Partition Molecule dialog. The LogP should be 6.48.

In the Distance Function... dialog turn the Steric Term on and press OK. Turn Save HintTables for each Row to on if, as in this case, you wish to examine in detail the results. Select all of the interaction subtypes (Total HINT Score, etc.) in the lower right hand region of the dialog. The interaction subtypes thus selected will be added to the table as individual labelled columns. The other options in the lower region of the dialog are reasonable in their default conditions.

Press OK to begin the column fill. This will take several minutes. You can see the scores for each row printed in the SYBYL text window. The program also prints the name of the HintTable file being created for that row.

These results can be analyzed in a variety of ways. Perhaps the best first look is to graph the Total HINT Score vs. time to look for the conformations with the highest scores. Use Graph, Scatter... to initiate this command. Then select hint_tot_6 as the Y Axis Column and Omit Axis as the Z Axis column. It is probably best to use Uniform Color. (Press Create.) Three conformations have particularly high scores. Identify them by pressing Pick Points on the Spreadsheet menubar. The leftmost is the initial (crystallographic) conformation, while the other two are at rows 46 and 68. Neither of these are substantially different in score from the initial, but we may want to minimize these complexes to see what their scores would look like at temperature equilibrium. (They actually decrease significantly in the present case.) We could also examine in detail the HINT Output tables for the target conformations. They are HintOut_46.tab and HintOut_68.tab, respectively.

This is obviously a contrived example that doesn't actually yield a useful result on this data set. The intention was to demonstrate how HintScore could be coupled with any procedure that generates multiple conformations for a single ligand.

The HINTMAPMSS column type is available to graphically analyze the results` of a dynamics or other run that produces multiple conformations. The idea was that, using this set of tools, one could create a "movie" showing how a complex or individual molecule responds to dynamics.