Institute for Biocomputation and Physics of Complex Systems of the University of Zaragoza

0.- Introduction

  • Biomolecules and their properties
  • Structural databases of ¬†biomolecules
  • Structure-energy relationship: Biomolecules modelling

1.- Potential energy surfaces in biomolecules

  • Intermolecular forces
  • Quantum Mechanics (QM)
  • Molecular Mechanics (MM): force fields
  • Mixed QM/MM models
  • Coarse grain models
  • Solvation models

2.- Conformational exploration

  • Minimization: reaction coordinate
  • Molecular dynamics and Monte carlo methods
  • Structure prediction methods

3.- Enzymatic catalysis

  • Basic concepts in enzymatic catalysis
  • Modelling enzymatic reactivity

4.- Protein-ligand interaction

  • Docking techniques
  • Calculation of binding free energies