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Transcript of Http:// Slide 1 CheVi Tutorial Aniko Simon, Darryl Reid, Sing Yoong Khew, and Zsolt Zsoldos...
http://www.simbiosys.ca Slide 1
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
http://www.simbiosys.ca Slide 2
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
http://www.simbiosys.ca Slide 3
Running and analysing in CheViRunning and analysing in CheViEstrogen Complex - 1ERREstrogen Complex - 1ERR
http://www.simbiosys.ca Slide 4
CheVi Opening Screen
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.
http://www.simbiosys.ca Slide 6
To start a new eHiTS run from CheVi click“New eHiTS Docking” button
http://www.simbiosys.ca Slide 7
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
http://www.simbiosys.ca Slide 8
Each Tab controls a different set of eHiTS OptionsFor more information about the setting see the eHiTS manual
http://www.simbiosys.ca Slide 9
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
http://www.simbiosys.ca Slide 10
Once the job has completed you can click on “View Results”
http://www.simbiosys.ca Slide 11
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
http://www.simbiosys.ca Slide 13
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.
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 thefragments. Click on the Rigid Fragments sub-menu under the Molecule.
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.
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 ligandand the receptor.
http://www.simbiosys.ca Slide 17
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.
http://www.simbiosys.ca Slide 18
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.
http://www.simbiosys.ca Slide 19
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
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.
http://www.simbiosys.ca Slide 21
The Surface Difference can have interactiontypes turned on and off by checking them in the table. Here only the polar interactionsare turned on.
http://www.simbiosys.ca Slide 22
Here we can see all the hydrophobic interactionsbetween the ligand and receptor.
http://www.simbiosys.ca Slide 23
The surface difference can also be colored by score.
http://www.simbiosys.ca Slide 24
Adjusting the scale can bring weakerinteractions to light.
http://www.simbiosys.ca Slide 25
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: [email protected]@simbiosys.ca for more for more information.information.
http://www.simbiosys.ca Slide 26
Thank you!Thank you!
Thank you for trying CheVi!
For more information please visit:
www.simbiosys.ca