The 'Science' Training

Central to the 'science' section of the course is the concept of the structure-based drug-design cycle. This is used as a unifying framework for all the course material. The cycle will be introduced to the student as a series of linked sections, starting from a 'simple', traditional medicinal chemistry perspective, and building up, through the addition of more explicit structural information to a full structure-based approach.

The concepts in the course will be tied to literature examples, giving the students the chance to explore areas in greater depth if required.

The 'science' training aims to:

Allow the student to rapidly analyze and characterize a protein structure
Introduce the student to the principles of molecular interactions
Explore the conformational flexibility possible for a ligand
Dock a ligand to a protein receptor
Design a ligand against a particular protein active site

Material covered:

• The Drug Design Cycle
  • The structure-based drug design cycle
• Molecular databases
  • Cambridge small molecule database
  • Protein structure databases
  • Enzyme databases
  • Protein sequence databases
• Molecular interactions
  • non-bonded interactions
  • hydrogen bonds
  • the hydrophobic effect
• Molecular mechanics
  • Force fields
  • Minimisation
  • Conformational searching
  • MO techniques
• Protein Structure
  • primary structure
  • tertiary structure
  • quaternary structure
  • structure comparison
  • experimental determination of protein structures (NMR and X-ray)
  • structure analysis
  • binding-site characterisation analysis
• Protein modelling
  • protein sequence searching and alignment
  • homology modelling
• Ligand binding
  • thermodynamics of ligand binding
  • solvation and desolvation
  • ligand docking
  • minimisation of ligand complexes
• Ligand Design
  • automated ligand design

Creation Date: 24th October 1995