The document provides an overview of molecular docking, which simulates the interaction between a candidate ligand and a receptor to predict binding modes and affinities. It discusses various docking methods, including flexible and rigid docking, and highlights the physical forces that drive ligand-receptor binding. Additionally, it mentions different computational approaches used in docking, such as shape-based methods, Monte Carlo simulations, and genetic algorithms.

1. Dr Mahavir H Ghante
Docking simplified

2. Molecular docking & algorithms
•Virtual screening approach to predict receptor-ligand binding modes
•“Docking is the computational simulation of a candidate ligand to a
receptor.”
•In the field of molecular modeling, docking is a method which predicts
the preferred orientation of one molecule to a second when bound to
each other to form stable complex.
•Scoring method used to detect correct bound conformation during
docking process to estimate binding affinities of candidate molecule
after completion of docking
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4. Molecular flexibility
•Flexible docking--both ligand and protein rigid
•flexible ligand and rigid protein
•Rigid docking--both ligand and protein flexible

5. • Ligand-receptor binding is driven by
• Electrostatics (including H-bonding)
• Dispersion of VDW’s forces
• Hydrophobic interaction
• Desolvation of ligand and receptor

6. How do my ligands dock into the protein?
• Various approaches, including:
• Shape (DOCK program)
• incremental search methods (Flex X)
• Monte Carlo/Simulated annealing (AUTODOCK, FLO)
• Genetic algorithms (GOLD)
• Molecular dynamics
• Systematic search (Glide, Open Eye)