BB2280 Molecular Modeling 7.5 credits

• Educational level

  Second cycle

• Academic level (A-D)

  D

• Subject area

  Biotechnology
  

• Grade scale

  A, B, C, D, E, FX, F

• Course page on KTH Social

Learning outcomes

Today, computer simulations are an important tool for the study of chemical processes in such different systems as isolated molecules, fluids, polymers, solid state, and biological macromolecules, like proteins and DNA.  The enormous development of computer hard drive space means that the molecular modeling field is developing very quickly. 

The goal with this course is to provide an overview of the methods and techniques which are used within modern molecular modeling.  Basic theory will be covered and applications within chemistry, biochemistry and medicinal chemistry will be discussed.

Course main content

The course consists of both theoretical lectures and practical computer exercises. The following topics will be discussed:

• Basic quantum chemistry: Molecular orbital theory, semi-empirical methods
• Basic density functional theory (DFT)
• Molecular mechanics and molecular dynamics
• Monte Carlo methods
• Energy minimization and potential energy surfaces
• QM/MM methods
• Solvation and surrounding effects
• Theoretical methods in drug discovery: Docking, protein structure prediction, QSAR
• Simulation of chemical reactions in solution
• Modelling of enzymatic catalysis
• Field trip to pharmaceutical company

Eligibility

At least 150 credits from grades 1, 2 and 3 of which at least 100 credits from years 1 and 2, and degree project, first level, must be completed. 

The 150 credits should include a minimum of 20 credits within the fields of Mathematics, Numerical Analysis and Computer Sciences, 5 of these must be within the fields of Numerical Analysis and Computer Sciences, 20 credits of Chemistry, possibly including courses in Chemical Measuring Techniques and 20 credits of Biotechnology or Molecular Biology

Prerequisites

Basic classes in chemistry and mathematics för K och BIO.

Literature

Andrew JR. Leach: Molecular Modelling, Principles and Applications, 2ed, and handouts.

Examination

• LAB1 - Laboratory Work, 1.5 credits, grade scale: A, B, C, D, E, FX, F
• TEN1 - Examination, 6.0 credits, grade scale: A, B, C, D, E, FX, F

Requirements for final grade

Home examination (TEN1, 6,0 credits, grading scale A-F) and Lab courses (LAB1, 1,5 credits, grading scale A-F).

Offered by

BIO/Biotechnology

Examiner

Hans Ågren <hagren@kth.se>

Supplementary information

Students are required to sign up at least two weeks in advance for examination.

The course is given provided at least seven students are admitted.

Version

Course plan valid from: Autumn 11.
Examination information valid from: Autumn 07.