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CheVi TutorialCheVi Tutorial

Aniko Simon, Darryl Reid, Aniko Simon, Darryl Reid, Sing Yoong Khew, and Zsolt ZsoldosSing Yoong Khew, and Zsolt Zsoldos

SimBioSys presentsSimBioSys presents

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OverviewOverview

CheVi (CheVi (CheChemical mical ViVisualizer) is a sualizer) is a visualization tool designed to show the visualization tool designed to show the interactions between ligands and interactions between ligands and receptorsreceptors

This tutorial will show you many of the This tutorial will show you many of the basic features of CheVi basic features of CheVi

For more advanced feature please see For more advanced feature please see the CheVi user manualthe CheVi user manual

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Running and analysing in CheViRunning and analysing in CheViEstrogen Complex - 1ERREstrogen Complex - 1ERR

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CheVi Opening Screen

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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.

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To start a new eHiTS run from CheVi click“New eHiTS Docking” button

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All docking options can be selectedvia these tabs, this demo will only use the basic -complex option

Click the Receptor Browse to select your complex file, 1err.pdb

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Each Tab controls a different set of eHiTS OptionsFor more information about the setting see the eHiTS manual

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In this example we are docking a complexand allowing eHiTS to automaticallysplit it and re-dock the ligand

Click the “Complex” check box

Click “Run eHiTS” to start your eHiTS Job

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Once the job has completed you can click on “View Results”

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The Top Ranked pose is shown for the ligand. With a table of informationabout that pose

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Docked Poses (green) and the crystalpose (pink) can be overlayed by clickingon the Ligand option in the menu. The receptor can also be shown in a similarmanner

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Docked poses can be superimposed byclicking the superimpose button on each pose you wish to see. Then click on thenext molecule and click Superimpose again.The list of superimpose molecules can beseen in the table.

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EHiTS works by docking rigid fragments in the receptor site. CheVi allows you to view the fragments and the chemical properties on thefragments. Click on the Rigid Fragments sub-menu under the Molecule.

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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.

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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 ligandand the receptor.

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The coloring by surface point type can be turnedoff by unchecking the option. Here the “frontface”of the surface has been turned off to allow youto see the ligand.

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Looking again at the surface of the ligand, each surface pointtype can be turned on or off usingthe table below. Here we see just the hydrogen bonding sites.

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Key interactions between the ligand and receptor can be shownwith interaction line. This can bedone by clicking “receptorinteractions” sub-menu under ligand molecules.

The score and distance can beshown by displaying the labels, choosing a specific interaction from the pull-down menu and selecting the distance and score buttons

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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.

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The Surface Difference can have interactiontypes turned on and off by checking them in the table. Here only the polar interactionsare turned on.

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Here we can see all the hydrophobic interactionsbetween the ligand and receptor.

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The surface difference can also be colored by score.

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Adjusting the scale can bring weakerinteractions to light.

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SummarySummary

The features shown in this tutorial are The features shown in this tutorial are only a fraction of those available in only a fraction of those available in CheVi.CheVi.

CheVi is under active development and CheVi is under active development and new features are added all the time.new features are added all the time.

Please check the CheVi manual or Please check the CheVi manual or website for the most up to date feature website for the most up to date feature listing or contact us at: listing or contact us at: support@simbiosys.casupport@simbiosys.ca for more for more information.information.

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Thank you!Thank you!

Thank you for trying CheVi!

For more information please visit:

www.simbiosys.ca