Dr. Chandra Anjaiah

TYPES OF MOLECULAR DOCKING
The experimentation
Search Algorithm: The experimentation
method determines the binding modes and
number of configurations creates. For docking
analysis, the Monte Carlo method, fragment and
genetic based, systemic searches is applied.
method determines the binding modes and
number of configurations creates. For docking
analysis, the Monte Carlo method, fragment and
genetic based, systemic searches is applied.
based scoring function uses
the statistics of the observed inter-atomic
contact frequencies in a large database of
the crystal structure of protein-ligand
complexes. Molecular interactions close to
the maximum frequency of interactions in
base will have a high binding
. A molecular interaction with
a. Rigid Docking
b. Flexible Docking
In this docking the receptor
2. Rigid Docking: In this docking the receptor
and ligand molecule both are fixed. Docking is
performed.
and ligand molecule both are fixed. Docking is
In this docking the ligand
and the receptor both are movable. It is
conformationally flexible. Each rotation the
mation surface
3. Flexible Docking: In this docking the ligand
and the receptor both are movable. It is
conformationally flexible. Each rotation the
energy is calculated. Each conformation surface
cell occupancy is calculated. After that the most
optimum binding pose is selected.
cell occupancy is calculated. After that the most
binding affinity is
4. Scoring Function: The binding affinity
directly corresponding to the binding score. The
best binders are best scoring ligands. It can be
experimental,
corresponding to the binding score. The
best binders are best scoring ligands. It can be
knowledge
knowledge
and
and
molecular
molecular
mechanics based. Docking Scoring is play
important role in designing of drug:
mechanics based. Docking Scoring is play
important role in desi