Iview bioinformatics tool for visualization for protein ligand complex........CADD/DOCKING

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2. AYESHA AFTAB MALIK
KHADIJA IJAZ
ZAHRA HANIF
DEPARTMENT OF BIOINFORMATICS AND TECHNOLOGY
INTERNATIONAL ISLAMIC UNIVERSITY ISLAMABAD
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3. RESEARCH PAPER DETAILS
• NAME: IVIEW: AN INTERACTIVE WEBGL VISUALIZER FOR PROTEIN-
LIGAND COMPLEX
• AUTHORS: HONG JIAN LI, KWONG-SAK LEUNG , TAKANORI NAKANE
AND MAN-HON WONG , DEPARTMENT OF COMPUTER SCIENCE AND
ENGINEERING, CHINESE UNIVERSITY OF HONG KONG, HONG KONG,
CHINA. 2GRADUATE SCHOOL OF MEDICINE, KYOTO,UNIVERSITY,
KYOTO, JAPAN.
• PUBLISHED IN: LI ET AL. BMC BIOINFORMATICS 2014
• 25 FEBRUARY 2014
• HTTP://WWW.BIOMEDCENTRAL.COM/1471-2105/15/56
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4. IVIEW

5. IVIEW
• AN INTERACTIVE WEBGL VISUALIZER FOR PROTEIN-LIGAND COMPLEX
SOFTWARE.
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6. BACKGROUND
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7. WHY VISUALIZATION TOOL IS
IMPORTANT?
PROTEIN-LIGAND COMPLEX PLAYS AN IMPORTANT
ROLE IN
• ELABORATING PROTEIN-LIGAND INTERACTIONS
•AIDING NOVEL DRUG DESIGN.
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8. ALREADY EXISTING TOOLS
 VISUALIZATION TOOLS:VMD,PYMOL
 DOCKING TOOLS,AUTODOCK,AUTODOCK VINA , IDOCK
 2D DIAGRAM PLOTTING TOOLS:POSEVIEW ,LIGPLOT
 WEB VISUALIZERS:GIANT
 CHEMINFORMATICS LIBRARY:CHEMDOODLEWEB COMPONENTS
 MOLECULAR VIEWER: GLMOL
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9. DRAWBACKS OF EXISTING
SOFTWARES
•SLOW SOFTWARE RENDERING
•LACK VIRTUAL REALITY SUPPORT.
•MACROMOLECULAR SURFACE CONSTRUCTION UNAVAILABLE.
•THE SUPPORT FOR PDBQT FORMAT IS NOT IMPLEMENTED.
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10. IMPLEMENTATION
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11. FILE FORMAT INPUT
 PDB
 PDBQT
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12. FEATURES
• CAMERA
• BACKGROUND
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13. CAMERA
 PERSPECTIVE
 ORTHOGRAPHIC
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14. CAMERA PERSPECTIVE
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15. ORTHOGRAPHIC
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16. BACKGROUND
 BLACK
 GREY
 WHITE
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17. GREY
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18. WHITE
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19. STRUCTURE COLORING
 ATOM SPECTRUM
 PROTEIN CHAIN
 PROTEIN SECONDARY
STRUCTURE
 B FACTOR
 RESIDUE NAME
 RESIDUE POLARITY
 ATOM TYPE 4/18/2014 19

20. PRIMARY STRUCTURE
 LINE
 STICK
 BALL & STICK
 SPHERE
 DOT
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21. PRIMARY STRUCTURE AS LINE
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22. PRIMARY STRUCTURE AS STICK
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23. PRIMARY STRUCTURE AS BALL AND
STICK
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24. DISPLAY IONS AS SPHERE
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25. IONS AS DOT
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26. SECONDARY STRUCTURE
 RIBBON
 STRAND
 CYLINDER & PLATE
 C ALPHA TRACE
 B FACTOR TUBE
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27. SECONDARY STRUCTURE AS RIBBON
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28. SECONDARY STRUCTURE AS STRAND
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29. SECONDARY STRUCTURE AS CYLINDER
AND PLATE
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30. C ALPHA TRACE
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31. B FACTOR TUBE
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32. PROTEIN SURFACE
 VAN DER WAALS SURFACE
 SOLVENT EXCLUDED SURFACE
 SOLVENT ACCESSIBLE SURFACE
 MOLECULAR SURFACE
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33. VANDER WALLS SURFACE
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34. SOLVENT EXCLUDED SURFACE
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35. SOLVENT ACCESSIBLE SURFACE
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36. MOLECULAR SURFACE
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37. PROTEINS SURFACE OPACITY
 1.0
 0.9
 0.8
 0.7
 0.6
 0.5
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38. PROTEIN SURFACE WIREFRAME
 YES
 NO
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39. WITH WIRE FRAME WORK
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40. ATOM AND RESIDUE LABELING
 YES
 NO
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41. LABELLED RESIDUES
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42. LIGAND VISUALIZATION
• LINE
• STICK
• BALL AND STICK
• SPHERE
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43. LIGAND AS LINE
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44. LIGAND AS STICK
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45. LIGAND AS BALL AND STICK
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46. LIGAND AS SPHERE
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47. VIRTUAL REALITY EFFECT
 ANAGLYPH
 PARALLAX BARRIER
 OCULUS RIFT
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48. ANAGLYPH
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49. PARALLAX BARRIER
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50. OCULUS RIFT
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51. RESULTS
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example the CCR5 chemokine receptor-
HIV entry inhibitor maraviroc complex

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Figure shows the human CCR5 secondary structure
rendered as ribbon, and the ligands rendered as
sphere.

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Figure shows the anaglyph effect in a virtual reality
environment. When users wear a spectacle with special
filters on both sides, the disparity between two superimposed
molecules creates a perception of depth, leading to
visually more appealing identification of intermolecular
interactions.

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Figure shows the protein surface generated by our
JavaScript implementation of the EDTSurf algorithm.
The human CCR5 is rendered as molecular surface
colored by chain. The marketed HIV drug maraviroc is
rendered as stick colored by chain. It can be clearly seen
that the asymmetric unit is composed of two
complexes,and the CCR5 forms a deep allosteric cavity
where maraviroc binds.

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successfully tested iview in:
Chrome 30,
Firefox 25
Safari 6.1
Opera 17.
Refer to http://caniuse.com/webgl, for compatibility of WebGL
support in desktop and mobile browsers.

56. CONCLUSION
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Iview is designed and developed to :
•Be a simple & straightforward way to visualize
protein-ligand complex.
•enables non-experts to quickly elucidate protei-
ligand interactions in a 3D manner.
• be a free and open source
•Easily integrated into any bioinformatics
application that requires interactive protein-
ligand visualization

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