Iview bioinformatics tool ....CADD/DOCKING

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AYESHA AFTAB MALIKKHADIJA IJAZZAHRA HANIF

DEPARTMENT OF BIOINFORMATICS AND TECHNOLOGYINTERNATIONAL ISLAMIC UNIVERSITY ISLAMABAD

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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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IVIEW

• AN INTERACTIVE WEBGL VISUALIZER FOR PROTEIN-LIGAND COMPLEX SOFTWARE.

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BACKGROUND

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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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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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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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IMPLEMENTATION

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FILE FORMAT INPUT

PDB

PDBQT

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FEATURES

• CAMERA

• BACKGROUND

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CAMERA

PERSPECTIVE

ORTHOGRAPHIC

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CAMERA PERSPECTIVE

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ORTHOGRAPHIC

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BACKGROUND

BLACK

GREY

WHITE

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GREY

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WHITE

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STRUCTURE COLORING

ATOM SPECTRUM

PROTEIN CHAIN

PROTEIN SECONDARY STRUCTURE

B FACTOR

RESIDUE NAME

RESIDUE POLARITY

ATOM TYPE

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PRIMARY STRUCTURE

LINE

STICK

BALL & STICK

SPHERE

DOT


PRIMARY STRUCTURE AS LINE


PRIMARY STRUCTURE AS STICK

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PRIMARY STRUCTURE AS BALL AND STICK


DISPLAY IONS AS SPHERE


IONS AS DOT

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SECONDARY STRUCTURE RIBBON

STRAND

CYLINDER & PLATE

C ALPHA TRACE

B FACTOR TUBE


SECONDARY STRUCTURE AS RIBBON

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SECONDARY STRUCTURE AS STRAND

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SECONDARY STRUCTURE AS CYLINDER AND PLATE

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C ALPHA TRACE

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B FACTOR TUBE

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PROTEIN SURFACE

VAN DER WAALS SURFACE

SOLVENT EXCLUDED SURFACE

SOLVENT ACCESSIBLE SURFACE

MOLECULAR SURFACE

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VANDER WALLS SURFACE

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SOLVENT EXCLUDED SURFACE

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SOLVENT ACCESSIBLE SURFACE

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MOLECULAR SURFACE

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PROTEINS SURFACE OPACITY

1.0

0.9

0.8

0.7

0.6

0.5

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PROTEIN SURFACE WIREFRAME

YES

NO

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WITH WIRE FRAME WORK

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ATOM AND RESIDUE LABELING

YES

NO

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LABELLED RESIDUES

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LIGAND VISUALIZATION

• LINE

• STICK

• BALL AND STICK

• SPHERE

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LIGAND AS LINE

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LIGAND AS STICK

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LIGAND AS BALL AND STICK

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LIGAND AS SPHERE

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VIRTUAL REALITY EFFECT

ANAGLYPH

PARALLAX BARRIER

OCULUS RIFT

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ANAGLYPH

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PARALLAX BARRIER


OCULUS RIFT

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RESULTS

example the CCR5 chemokine receptor-HIV entry inhibitor maraviroc complex

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Figure shows the human CCR5 secondary structurerendered as ribbon, and the ligands rendered assphere.

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Figure shows the anaglyph effect in a virtual realityenvironment. When users wear a spectacle with specialfilters on both sides, the disparity between two superimposedmolecules creates a perception of depth, leading tovisually more appealing identification of intermolecularinteractions.

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Figure shows the protein surface generated by ourJavaScript 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 25Safari 6.1 Opera 17.Refer to http://caniuse.com/webgl, for compatibility of WebGL support in desktop and mobile browsers.

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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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Iview bioinformatics tool ....CADD/DOCKING

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