Biomolecular Simulation in Medicinal Chemistry and Toxicology


Course Objective

Providing theoretical background on biomolecular simulation and
free-energy calculation methods and an overview of recent developments,
applications, and trends.

Course Content

Methods and techniques for calculating molecular energies of
biomolecular systems (molecular mechanics / force fields) and for
flexibility analysis (conformational search methods).
Theory (statistical mechanics), method development (algorithms) and
application of molecular dynamics simulations and free energy
Proper and efficient treatment of nonbonded intereactions: force field
development, boundary
conditions, long-range forces.
Analysis of simulation data: secondary structure, solvation and
thermodynamic properties, transport and correlation.
Special focus on methods to predict binding affinities from MD
simulation (thermodynamic integration, free energy perturbation) and
their application.

Teaching Methods

Lectures, tutorials, exercises, and self-study.

Method of Assessment

Written or oral exam

Entry Requirements

Course "Computational Design and Synthesis of Drugs"


Leach, A.R., Molecular Modelling: Principles and Applications. (ISBN
Recent review articles that will be made available via Canvas.

Target Audience


Additional Information

Please contact the coordinator two weeks prior to the start of the
course (e-mail:

Recommended background knowledge

Course "Computational Design and Synthesis of Drugs"

General Information

Course Code X_432664
Credits 6 EC
Period P5+6
Course Level 400
Language of Tuition English
Faculty Faculty of Science
Course Coordinator dr. D.P. Geerke
Examiner dr. D.P. Geerke
Teaching Staff dr. D.P. Geerke
dr. C. de Graaf

Practical Information

You need to register for this course yourself

Last-minute registration is available for this course.

Teaching Methods Lecture
Target audiences

This course is also available as: