C8 – Molecular modelling of enzymatic catalysis
Key information
Next planned course: April 15-19 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.
Course participants must register in two ways:
- Register to BioCat using the form at the bottom of this page
- Register through UiT, the host university
- UiT students must register through studentweb
- Non-UiT students must request guest status from UiT
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.
Register through BioCat
Registration is now closed
