C8 – Molecular modelling of enzymatic catalysis

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Key information

Next planned course: Spring 2024
Location: UiT
Course responsible: Bjørn Olav Brandsdal

Grading: Assignments (50%) and oral exam (50%) (pass/fail)
Credits: 6 ECTS 

Note! This is a scaled down version of the course that was previously offered over two weeks for 10 credit points.

Registration

Important! Registration is binding! Do not register for a course unless you are sure that you can attend.

Registration through this course will have to be done at your home institution (for all universities, UiT included) as a special curriculum. BioCat will issue Certificates of Completion to those who pass the course so that their credits can be entered manually by their home administration.

Please also register to BioCat using the form at the bottom of this page so we know how many students to expect and we have your contact information.

Content

The course will present central methods in molecular modeling for the analysis of enzyme structure-function relationship and the modeling of their catalytic activity.

Teaching

This course will be held over one week at UiT. The syllabus and work plan is in the process of being updated, but see the details below to get an idea of what is to come (subject to revision).

Day 1

  • D1: Computational methods for the investigation of structure-function relationships of enzymes
  • D2: Force fields (FF)
  • D3: Geometry optimization/Molecular simulations
  • D4: Enhanced sampling methods
  • D5: Normal mode analysis

Days 2-5

  • D1: Docking
  • D2: Free energy calculations
  • D3: Empirical Valence Bond (EVB)
  • D4: Quantum mechanical calculations for the purpose of FF/EVD parameterization
  • D5: Validation of computer simulations

Work requirement

The students will be given two independent assignments to work on. Each project will require that the students perform computations on their own and will be independent of the exercises done during the hands-on session.

Exam and evaluation

Assignments will count for 50% of the final evaluation. Oral exam will count for the other half.

Registration

Registration is now closed.