These animations show the docked conformations generated by 100 independent runs of AutoDock version 2.4. In each case, the crystallographic conformation is represented in green. Each atom of a docked conformation samples an intermolecular atomic affinity grid and a color is assigned to each atom based on the color range shown. Atoms with repulsive energies thus appear red, while those with attractive energies are blue. Hence the coloring changes depending on the conformation. The sampling method does not take into account the atom type: for example, if the ligand is sampling a carbon-affinity grid, hydrogen atoms are colored as if they were carbon atoms. Note that only polar hydrogens are explicitly treated; non-polar hydrogens are "unified" with their parent heavy atom, by increasing the heavy atom's van der Waals' radius.
The molecular surface of each protein was calculated using MSMS, Michel Sanner's molecular surface program. The MPEG movies were generated using AVS, with a version of the "Create_MPEG" module, modified for the 64-bit DEC Alpha platform. The original version of the Create_MPEG module came from the International AVS Center (IAC).
It is worth emphasizing here that each frame in these animations shows the result of a separate AutoDock run. Each of these runs began with the ligand in a completely random translation, random orientation and, where appropriate, random torsion. We are not seeing trajectories of the ligand during a docking (although this is possible with AutoDock).
The docked conformations are sorted in order of increasing energy, so the lowest energy docked conformation is the first frame in every movie. Note how well this corresponds with the crystallographic coordinates of the ligand.
691K MPEG.
Every atom of the ligand, benzamidine, is color coded by C-atom affinity.
The blue color of the phenyl ring indicates that it has a favorable
interaction energy in all the 100 dockings. Note the NH2 groups
are colored red; these atoms are also sampling the carbon affinity grid,
even though they do not in the actual dockings: this is a limitation of the
"sample" module in AVS. The crystallographic coordinates of
benzamidine are shown in green.
1,585K MPEG.
The color coding is by carbon-atom affinity.
The crystallographic coordinates of camphor are shown in green. Also
shown are the heme moiety and Tyr-96, which donates a hydrogen bond to
camphor. The backbone of cytochrome P-450cam is represented by ribbons,
which was generated by an AVS module written by Alex Shah, around Mike
Carson's Ribbons code. Note the slight unwinding of the proximal helix, I,
which helps form the dioxygen binding pocket, to the right of this picture.
1,077K MPEG.
Note the transparent bluish
pockets of oxygen affinity, which is iso-contoured at -2.5 kcal/mol. The
phosphocholine molecule is coloured by oxygen affinity, also. Compared
to the camphor and benzamidine dockings, there is much wider spread of
final docked conformations, although the lowest energy cluster is the
one which corresponds most closely to the observed conformation, shown in
green.
884K MPEG.
This movie shows the ligand biotin and its final docked conformations after
100 AutoDock dockings to streptavidin. Like all the other movies on this
page, the order of conformations in this animation is from lowest energy to
highest. The crystal structure conformation of biotin is shown in green.
Note the beautiful, elongated binding cleft. To give an idea of scale,
the sides of the grid shown in the background are 22.875 Å long.
899K MPEG.
Here we can see how a large inhibitor binds to HIV-1 protease. The inhibitor
in question is a Merck-Dupont compound, XK-263, which consists of a 7-membered
cyclic urea moiety, with phenyl and naphthyl rings branching off. The cyclic
carbonyl oxygen mimics the water-301 which is structurally conserved, but is
displaced by this ligand. The lower part of the cyclic urea ring has two
adjacent hydroxyls that H-bond to the catalytic aspartates. Note that there
are a large number of docked conformations which do not gain access to the
tunnel of the active site, but instead find higher energy local minima near the
entrances. The crystal structure of the complexed protease inhibitor, XK-263,
is shown in green. The protease is represented by a ribbon diagram: the two
flaps run diagonally from upper left to lower right.
973K MPEG.
Sialic acid/hemagglutinin docking.
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