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Hydrogen Bonds Visualization  |  Collision Visualization  |  Energy Visualization  |   Scoring Function  |  Flexibility of Molecular Structure  |  Optimization

Interactive Docking  |  Binding Site Prediction  |  Solvent Excluded Surface


Movies

Protein-Protein Docking (20M)  |  Protein-Ligand Docking (19M)  | 


 


 Pictures 


Hydrogen Bonds Visualization



Big blue spheres represent water. Dashed-blue lines represent hydrogen bonds between
the ligand and a water molecule. Dashed-green lines represent hydrogen bonds between
ligand and receptor. Dashed-yellow lines represent intra-molecular hydrogen bonds.
The length of a hydrogen bond is shown along the dashed line.

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Collision Visualization



Red spheres represent intra-molecular collisions.  Yellow spheres represent
inter-molecular collisions. The radius of the collision sphere is proportional
to the penetration depth of the van-der-Waals spheres of the two intersecting
atoms (PDB code 2SEC).

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Energy Visualization



Volume Based                                                                                              

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Scoring Function



A snapshot of interactive docking. Pockets are visualized by sticks of different colors that represent different binding sites. The value of the score function is calculated. The total score is on the top. The first score is hydrophobicity. The second and third scores are the number of intra- and inter-molecular overlaps. The fourth and fifth scores are the number of intra- and inter-molecular hydrogen bonds (PDB code 4HVP).


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Flexibility of Molecular Structure



Selected beta strand and surrounding 3D manipulation widget.
Selected coil regions are activated for manipulation.

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Optimization






Interactive Docking



A snapshot of interactive docking. Rendering of HIV-1 Protease in Cmplex with
the Cyclic Sulfamide Inhibitor Aha006 (PDB code 1AJV).

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Binding Site Prediction



Van-Der-Waals spheres in different colors visualize different pockets.
The detection of
pockets in proteins is based on an analytical method,
to decide the binding sites.

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Solvent Excluded Surface



SOLVENT EXCLUDED SURFACE.

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Movies

Protein-Protein Docking (20M)  |  Protein-Ligand Docking (19M)  |