1. http://www.simbiosys.ca Slide 1 CheVi Tutorial Aniko Simon, Darryl Reid, Sing Yoong Khew, and Zsolt Zsoldos SimBioSys presents

2. http://www.simbiosys.ca Slide 2 Overview CheVi (Chemical Visualizer) is a visualization tool designed to show the interactions between ligands and receptors CheVi (Chemical Visualizer) is a visualization tool designed to show the interactions between ligands and receptors This tutorial will show you many of the basic features of CheVi This tutorial will show you many of the basic features of CheVi For more advanced feature please see the CheVi user manual For more advanced feature please see the CheVi user manual

3. http://www.simbiosys.ca Slide 3 Running and analysing in CheVi Estrogen Complex - 1ERR

4. http://www.simbiosys.ca Slide 4 CheVi Opening Screen

5. http://www.simbiosys.ca Slide 5 Before you can start running eHiTS docking jobs with CheVi, you must configure CheVi so it knows the location of your eHiTS installation. To do this Click Edit -> Configure. Enter the path to your eHiTS installation.

6. http://www.simbiosys.ca Slide 6 To start a new eHiTS run from CheVi click New eHiTS Docking button

7. http://www.simbiosys.ca Slide 7 All docking options can be selected via these tabs, this demo will only use the basic -complex option Click the Receptor Browse to select your complex file, 1err.pdb

8. http://www.simbiosys.ca Slide 8 Each Tab controls a different set of eHiTS Options For more information about the setting see the eHiTS manual

9. http://www.simbiosys.ca Slide 9 In this example we are docking a complex and allowing eHiTS to automatically split it and re-dock the ligand Click the Complex check box Click Run eHiTS to start your eHiTS Job

10. http://www.simbiosys.ca Slide 10 Once the job has completed you can click on View Results

11. http://www.simbiosys.ca Slide 11 The Top Ranked pose is shown for the ligand. With a table of information about that pose

12. http://www.simbiosys.ca Slide 12 Docked Poses (green) and the crystal pose (pink) can be overlayed by clicking on the Ligand option in the menu. The receptor can also be shown in a similar manner

13. http://www.simbiosys.ca Slide 13 Docked poses can be superimposed by clicking the superimpose button on each pose you wish to see. Then click on the next molecule and click Superimpose again. The list of superimpose molecules can be seen in the table.

14. http://www.simbiosys.ca Slide 14 EHiTS works by docking rigid fragments in the receptor site. CheVi allows you to view the fragments and the chemical properties on the fragments. Click on the Rigid Fragments sub- menu under the Molecule.

15. http://www.simbiosys.ca Slide 15 Scoring in eHiTS is by interacting surface points. The surfaces of molecules can be visualized colored by surface point type (chemical feature). Clicking on Surface sub-menu will show the surface.

16. http://www.simbiosys.ca Slide 16 A similar surface can be shown for the receptor. Click on the Surface sub-menu for the receptor. This will show the interactions between the ligand and the receptor.

17. http://www.simbiosys.ca Slide 17 The coloring by surface point type can be turned off by unchecking the option. Here the frontface of the surface has been turned off to allow you to see the ligand.

18. http://www.simbiosys.ca Slide 18 Looking again at the surface of the ligand, each surface point type can be turned on or off using the table below. Here we see just the hydrogen bonding sites.

19. http://www.simbiosys.ca Slide 19 Key interactions between the ligand and receptor can be shown with interaction line. This can be done by clicking receptor interactions sub-menu under ligand molecules. The score and distance can be shown by displaying the labels, choosing a specific interaction from the pull-down menu and selecting the distance and score buttons

20. http://www.simbiosys.ca Slide 20 The space between the ligand and the receptor, the Surface Difference can be visualized by clicking the Receptor Surface Difference menu option. This is shown colored by interaction type.

21. http://www.simbiosys.ca Slide 21 The Surface Difference can have interaction types turned on and off by checking them in the table. Here only the polar interactions are turned on.

22. http://www.simbiosys.ca Slide 22 Here we can see all the hydrophobic interactions between the ligand and receptor.

23. http://www.simbiosys.ca Slide 23 The surface difference can also be colored by score.

24. http://www.simbiosys.ca Slide 24 Adjusting the scale can bring weaker interactions to light.

25. http://www.simbiosys.ca Slide 25 Summary The features shown in this tutorial are only a fraction of those available in CheVi. The features shown in this tutorial are only a fraction of those available in CheVi. CheVi is under active development and new features are added all the time. CheVi is under active development and new features are added all the time. Please check the CheVi manual or website for the most up to date feature listing or contact us at: support@simbiosys.ca for more information. Please check the CheVi manual or website for the most up to date feature listing or contact us at: support@simbiosys.ca for more information.

26. http://www.simbiosys.ca Slide 26 Thank you! Thank you for trying CheVi! For more information please visit: www.simbiosys.ca