BIOE 460 - Molecular Modelling

Class Schedule

Spring term

Wednesday 12:30 - 15:20

Office Hours

Monday 13:30 - 15:30

Course Objectives

The aim of this course is to provide introduction to some of techniques used in molecular modelling and to illustrate how these techniques can be used to study physical, chemical and biological systems.

Textbook

· "Molecular Modelling: Principles and Applications", AR Leach

Grading Policy

Mid-term Exams : 20 % + 20 %

Homework sets : 20 %

Final Exam : 40 %

70 % attendance is required.

Syllabus

Ä click to download

Lecture Notes

Ä Introduction to molecular modelling

Ä Force fields. Energy calculation.

Ä Potential energy surface. Energy minimization.

Ä Dynamics of proteins. Normal mode analysis. Elastic network models.

Ä Computer simulation methods.

Ä Molecular Dynamics simulations.

Ä Monte Carlo simulation methods.

Ä Conformational analysis.

Ä Protein structure prediction.

Ä Molecular docking.

¸ Homework - I due on April 1

¸ Homework - II due on May 20

¸ Homework - III due on May 29