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Iview bioinformatics tool ....CADD/DOCKING

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

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Iview bioinformatics tool ....CADD/DOCKING

  1. 1. 4/18/2014Free template from www.brainybetty.com 1
  2. 2. AYESHA AFTAB MALIK KHADIJA IJAZ ZAHRA HANIF DEPARTMENT OF BIOINFORMATICS AND TECHNOLOGY INTERNATIONAL ISLAMIC UNIVERSITY ISLAMABAD 4/18/2014 2
  3. 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 4/18/2014 3
  4. 4. IVIEW
  5. 5. IVIEW • AN INTERACTIVE WEBGL VISUALIZER FOR PROTEIN-LIGAND COMPLEX SOFTWARE. 4/18/2014 5
  6. 6. BACKGROUND 4/18/2014 6
  7. 7. WHY VISUALIZATION TOOL IS IMPORTANT? PROTEIN-LIGAND COMPLEX PLAYS AN IMPORTANT ROLE IN • ELABORATING PROTEIN-LIGAND INTERACTIONS •AIDING NOVEL DRUG DESIGN. Free template from www.brainybetty.com 7
  8. 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 4/18/2014 8
  9. 9. DRAWBACKS OF EXISTING SOFTWARES •SLOW SOFTWARE RENDERING •LACK VIRTUAL REALITY SUPPORT. •MACROMOLECULAR SURFACE CONSTRUCTION UNAVAILABLE. •THE SUPPORT FOR PDBQT FORMAT IS NOT IMPLEMENTED. 4/18/2014 9
  10. 10. IMPLEMENTATION 4/18/2014 10
  11. 11. FILE FORMAT INPUT  PDB  PDBQT 4/18/2014 11
  12. 12. FEATURES • CAMERA • BACKGROUND 4/18/2014 12
  13. 13. CAMERA  PERSPECTIVE  ORTHOGRAPHIC 4/18/2014 13
  14. 14. CAMERA PERSPECTIVE 4/18/2014 14
  15. 15. ORTHOGRAPHIC 4/18/2014 15
  16. 16. BACKGROUND  BLACK  GREY  WHITE 4/18/2014 16
  17. 17. GREY 4/18/2014 17
  18. 18. WHITE 4/18/2014 18
  19. 19. STRUCTURE COLORING  ATOM SPECTRUM  PROTEIN CHAIN  PROTEIN SECONDARY STRUCTURE  B FACTOR  RESIDUE NAME  RESIDUE POLARITY  ATOM TYPE 4/18/2014 19
  20. 20. PRIMARY STRUCTURE  LINE  STICK  BALL & STICK  SPHERE  DOT 4/18/2014 20
  21. 21. PRIMARY STRUCTURE AS LINE 4/18/2014Free template from www.brainybetty.com 21
  22. 22. PRIMARY STRUCTURE AS STICK 4/18/2014Free template from www.brainybetty.com 22
  23. 23. PRIMARY STRUCTURE AS BALL AND STICK 4/18/2014 23
  24. 24. DISPLAY IONS AS SPHERE 4/18/2014Free template from www.brainybetty.com 24
  25. 25. IONS AS DOT 4/18/2014Free template from www.brainybetty.com 25
  26. 26. SECONDARY STRUCTURE  RIBBON  STRAND  CYLINDER & PLATE  C ALPHA TRACE  B FACTOR TUBE 4/18/2014 26
  27. 27. SECONDARY STRUCTURE AS RIBBON 4/18/2014Free template from www.brainybetty.com 27
  28. 28. SECONDARY STRUCTURE AS STRAND 4/18/2014 28
  29. 29. SECONDARY STRUCTURE AS CYLINDER AND PLATE 4/18/2014 29
  30. 30. C ALPHA TRACE 4/18/2014 30
  31. 31. B FACTOR TUBE 4/18/2014 31
  32. 32. PROTEIN SURFACE  VAN DER WAALS SURFACE  SOLVENT EXCLUDED SURFACE  SOLVENT ACCESSIBLE SURFACE  MOLECULAR SURFACE 4/18/2014 32
  33. 33. VANDER WALLS SURFACE 4/18/2014 33
  34. 34. SOLVENT EXCLUDED SURFACE 4/18/2014 34
  35. 35. SOLVENT ACCESSIBLE SURFACE 4/18/2014 35
  36. 36. MOLECULAR SURFACE 4/18/2014 36
  37. 37. PROTEINS SURFACE OPACITY  1.0  0.9  0.8  0.7  0.6  0.5 4/18/2014 37
  38. 38. PROTEIN SURFACE WIREFRAME  YES  NO 4/18/2014 38
  39. 39. WITH WIRE FRAME WORK 4/18/2014 39
  40. 40. ATOM AND RESIDUE LABELING  YES  NO 4/18/2014 40
  41. 41. LABELLED RESIDUES 4/18/2014 41
  42. 42. LIGAND VISUALIZATION • LINE • STICK • BALL AND STICK • SPHERE 4/18/2014 42
  43. 43. LIGAND AS LINE 4/18/2014 43
  44. 44. LIGAND AS STICK 4/18/2014 44
  45. 45. LIGAND AS BALL AND STICK 4/18/2014 45
  46. 46. LIGAND AS SPHERE 4/18/2014 46
  47. 47. VIRTUAL REALITY EFFECT  ANAGLYPH  PARALLAX BARRIER  OCULUS RIFT 4/18/2014 47
  48. 48. ANAGLYPH 4/18/2014 48
  49. 49. PARALLAX BARRIER 4/18/2014 49
  50. 50. OCULUS RIFT 4/18/2014Free template from www.brainybetty.com 50
  51. 51. RESULTS 4/18/2014 51 example the CCR5 chemokine receptor- HIV entry inhibitor maraviroc complex
  52. 52. 4/18/2014 52 Figure shows the human CCR5 secondary structure rendered as ribbon, and the ligands rendered as sphere.
  53. 53. 4/18/2014 53 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.
  54. 54. 4/18/2014 54 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.
  55. 55. 4/18/2014 55 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. 56. CONCLUSION 4/18/2014 56
  57. 57. 4/18/2014 57 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
  58. 58. REFERENCES • HUMPHREY W, DALKE A, SCHULTEN K: VMD: VISUALMOLECULAR DYNAMICS. • JMOL GRAPH 1996, 14(1):33–38. • 2. PETTERSEN EF, GODDARD TD, HUANG CC, COUCH GS, GREENBLATT D. M, • MENG EC, FERRIN TE: UCSF CHIMERA - A VISUALIZATION SYSTEM FOR • EXPLORATORY RESEARCH AND ANALYSIS. J COMPUT CHEM 2004, • 25(13):1605–1612. • 3. MORRIS GM, HUEY R, LINDSTROM W, SANNER MF, BELEW RK, GOODSELL DS, • OLSON AJ: AUTODOCK4 AND AUTODOCKTOOLS4: AUTOMATED DOCKING WITH • SELECTIVE RECEPTOR FLEXIBILITY. J COMPUT CHEM 2009, 30(16):2785–2791. • 4. TROTT O, OLSON AJ: AUTODOCK VINA: IMPROVING THE SPEED AND ACCURACY • OF DOCKING WITH A NEW SCORING FUNCTION, EFFICIENT OPTIMIZATION, AND • MULTITHREADING. J COMPUT CHEM 2010, 31(2):455–461. • 5. LI H, LEUNG K-S, WONG M-H: IDOCK: AMULTITHREADED VIRTUAL SCREENING • TOOL FOR FLEXIBLE LIGAND DOCKING. IN 2012 IEEE SYMPOSIUM ON • COMPUTATIONAL INTELLIGENCE IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY • (CIBCB). SAN DIEGO, CALIFORNIA, USA: IEEE; 2012:77–84. [HTTP://IEEEXPLORE. • IEEE.ORG/XPL/ARTICLEDETAILS.JSP?ARNUMBER=6217214] • 6. TSE C-M, LI H, LEUNG K-S, LEE K-H, WONG M-H: INTERACTIVE DRUG DESIGN IN • VIRTUAL REALITY. IN 15TH INTERNATIONAL CONFERENCE ON INFORMATION • VISUALISATION (IV). LONDON, UK: IEEE; 2011:226–231. [HTTP://IEEEXPLORE.IEEE. • ORG/XPL/ARTICLEDETAILS.JSP?ARNUMBER=6004005] • 7. STIERAND K, RAREY M: POSEVIEW -MOLECULAR INTERACTION PATTERNS AT A • GLANCE. J CHEMINFORM 2010, 2:50. • 8. LASKOWSKI RA, SWINDELLS MB: LIGPLOT+:MULTIPLE LIGAND-PROTEIN • INTERACTION DIAGRAMS FOR DRUG DISCOVERY. J CHEM INFORMMODELING 2011, • 51(10):2778–2786. • 9. KASAHARA K, KINOSHITA K: GIANT: PATTERN ANALYSIS OF MOLECULAR • INTERACTIONS IN 3D STRUCTURES OF PROTEIN-SMALL LIGAND COMPLEXES. • BMC BIOINFORMATICS 2014, 15(1):12. • 10. HANSON RM, PRILUSKY J, RENJIAN Z, NAKANE T, SUSSMAN JL: JSMOL AND THE • NEXT-GENERATION WEB-BASED REPRESENTATION OF 3DMOLECULAR • STRUCTURE AS APPLIED TO PROTEOPEDIA. ISR J CHEM 2013, 53(3–4):207– 216. 4/18/2014 58
  59. 59. 4/18/2014Free template from www.brainybetty.com 59
  60. 60. 4/18/2014Free template from www.brainybetty.com 60

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

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