Molecular modelling Flashcards
What are the two types of computer-aided drug design?
Ligand Based Design
Structure Based Design
What is Ligand Based Design?
Computer Aided Drug Design where the structure of the molecular target is not known but the structures of a number of biologically active compounds are known
Give three examples of Ligand Based Design
QSAR
Pharmacophore
Shape-based applications
What is Structure Based Design?
Computer Aided Drug Design where the structure of the molecular target is known
Give two examples of Structure Based Design
Docking
De novo Drug Design
Why is the Lock and Key hypothesis unrealistic?
Protein and ligand are both flexible
- binding induces significant conformational changes
Give examples of non-bonded interactions
Ionic bonds
Hydrogen bonds
Dipole-Dipole interactions
Van der Waals interactions
Higher order multipole interactions
Give examples of methods that researchers use to suggest structures of targets
X-ray crystallography
NMR spectroscopy
Homology modelling
Cryo-EM computer based modelling
What is the Brookhaven Protein Database?
Contains X-ray and NMR structures of proteins
- >150,000 structures
