Molecular Docking and its types

1. Molecular Docking
HARENDRA BISHT
M. PHARMACY (2ND SEM)
DEPARTMENT OF PHARMACEUTICAL SCIENCE,
SIR J. C. BOSE TECHNICAL CAMPUS BHIMTAL
MAIL: HSB.BISHT40@GMAIL.COM
CONTACT: 8171232896

2. Definition
 Molecular docking is a computational method to predict the interaction of
two molecules generation a binding model (Drug-receptor complex) .
 In many drug discovery applications, docking is done between a small
molecule and a macromolecule for example 1) Protein-small molecule
(ligand) docking
2) Protein nucleic acid docking
3) Protein- protein docking
 Molecular docking is the study of how two or more molecular structures
(e.g., drug and enzyme or protein) fit together .
 In a simple definition, docking is a molecular modeling technique that is
used to predict how a protein (enzyme) interacts with small molecules
(ligands).

4. 3-D Structure of Drug-receptor complex:

5. Steps of Docking:
Step1: Start with crystal co-ordinates with target receptor.
Step2 : Generate molecular surface for receptor.
Step3 : Generate spheres to fill the active site of the receptor, the sphere
become potential locations for ligand atoms.
Step4 : Sphere centres are matched with the ligand atoms, to determine
possible orientation for the ligand.
Step5 : Find the top scoring or the best ranking.

6. General procedure for MD:

7. Docking assessment:
 Hydrophilic and hydrophobic interactions.
 Hydrogen bond donated
 Hydrogen bond accepted
 Ligand orientation with best Complementarity Score
 Binding Affinities
 Ionic interactions
 Aromatic interaction
 Vander-waals forces
 Electrostatic forces
 Free energies
Properties
calculated after
Docking
procedure

10. III. Manual Docking
 In manual docking, the ligand is placed in the interacting site and the
association energy is calculated at each step.
 The user manually moves, rotates or translates the compound inside the
protein cavity and docking assessment are recorded.

27. Thank you..