Key information

Next planned course: Spring 2022
Locations: UiB (week 1) & UiT (week 2)
Course responsible: TBD

Grading: Assignments (50%) and oral exam (50%) (pass/fail)
Credits: 10 ECTS 

Registration

All students must register to BioCat.

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

The course will be given over two weeks from 9 to 16 every day, not necessarily consecutive, and happening on two different sites (UiB and UiT). Mornings will be dedicated to lectures (3 hours) and afternoons to hands-on sessions (4 hours).

Week 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

Week 2 (35 hours lectures+hands on)

  • 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. One will focus on the learning outcomes from week #1 and the other one on the projects from week #2. 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. We estimate that each project will require about 3-5 days of work

Exam and evaluation

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