BB2280 Molecular Modeling 7.5 credits

Molekylär modellering

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Course information

Content and learning outcomes

Course contents *

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

Intended 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 Disposition

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Literature and preparations

Specific prerequisites *

Admission requirements for programme students at KTH:
At least 150 credits from grades 1, 2 and 3 of which at least 100 credits from years 1 and 2, and bachelor's work 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.

Admission requirements for independent students:
A total of 20 university credits (hp) in Biotechnology or Molecular Biology. 20 university credits (hp) of Chemistry, possibly including courses in Chemical Measuring Techniques , as well as 20 university credits (hp) in Mathematics,  Numerical Analysis and Computer Sciences, 5 of these must be within the fields of Numerical Analysis and Computer Sciences. Documented proficiency in English corresponding to English B.

Recommended prerequisites

Basic classes in chemistry and mathematics för K och BIO.

Equipment

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Literature

Andrew R. Leach: Molecular Modelling, Principles and Applications, 2ed, samt utdelat material.

Examination and completion

Grading scale *

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

Examination *

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

Based on recommendation from KTH’s coordinator for disabilities, the examiner will decide how to adapt an examination for students with documented disability.

The examiner may apply another examination format when re-examining individual students.

Other requirements for final grade *

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

Opportunity to complete the requirements via supplementary examination

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Opportunity to raise an approved grade via renewed examination

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Examiner

Mårten Ahlquist

Further information

Course web

Further information about the course can be found on the Course web at the link below. Information on the Course web will later be moved to this site.

Course web BB2280

Offered by

CBH/Theoretical Chemistry and Biology

Main field of study *

Biotechnology

Education cycle *

Second cycle

Add-on studies

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Ethical approach *

  • All members of a group are responsible for the group's work.
  • In any assessment, every student shall honestly disclose any help received and sources used.
  • In an oral assessment, every student shall be able to present and answer questions about the entire assignment and solution.

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.